title: osteoclast precursor, KO2

city: Sapporo

first: Ji-Won

last: Lee

state: Does Not Apply

address: N13W7, Kita-Ku

department: Graduate school of Dental Medicine

country: Japan

institute: Hokkaido University

data_processing:
Sequence reads were mapped to mm39 using STAR 2.7.8a (parameters: --twopassMode Basic, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --outSAMstrandField intronMotif, --outFilterIntronMotifs None, --alignSoftClipAtReferenceEnds Yes, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --chimOutType WithinBAM SoftClip, --chimMainSegmentMultNmax 1)_x000D_
For each gene in GENCODE v26, the counts of mapped reads were calculated using htseq-count (parameters: -i gene_id, -m intersection-nonempty, -r pos, -s no)
Read counts were normalized using DESeq2 (version 1.28.1)
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files includes raw counts and normalized read counts for each Sample

source_name: Bone

growth_protocol: Freshly harvested mouse bone marrow cells (BMCs) isolated from 8–10-week-old mice cultured in α-MEM (Gibco BRL, Gaithersburg, MD) were used as the source of osteoclasts.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Illumina TruSeq Standard mRNA Sample Prep Kit set A was used for the library preparation.

treatment_protocol: Bone marrow-derived macrophages (BMMs) were induced with M-CSF (50 ng/mL) at 6 cm dish for 15-18 hr incubation and differentiated into osteoclast with RANKL (50 ng/mL) for an additional 2 days.

value: Bone

value: Bone marrow

value: M-CSF for 2 days, RANKL for 2 days

tag: cell type (differentiated)

value: osteoclast precursors (pOCs)


title: osteoclast precursor, KO3

status: Public on Jul 18 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: tissue

tag: cell type

tag: treatment


title: osteoclast precursor, KO1


title: osteoclast precursor, WT3

value: WT


title: 9A_M_1109

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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-seq2

molecule: genomic DNA

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: osteoclast precursor, WT1


title: osteoclast precursor, WT2


title: 9A_M_1108


title: HCT116 cells, Vector 2

city: Guangzhou

first: Youwei

last: Huang

state: Guangdong

address: West Huangpu Avenue no.601

department: Department of pharmacology

country: China

institute: Jinan University

data_processing:
Illumina Casava1.4 software used for basecalling.
Data were filtered the low-quality sequences, including adapter sequence and low-quality bases (mass value ≤20) using the software FASTP.
Reads were referenced to the genome using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software.
Reads were calculated using fragments per kilobaseof exon per million fragments mapped (FPKM) software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Large intestine, Colon

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1× penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Large intestine, Colon

tag: cell line

value: Colorectal cancer cell

value: Vector


title: HCT116 cells, Vector 3


title: d106S-IL12-IL16

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral d106S-Il12 virus and IL6R blockade

data_processing:
FASTQs were aligned against the mm10 genome and gene-level counts were generated using the 10x CellRanger (v3.1.0) pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: MEX sparse matrix (Compressed) containing raw gene-level counts for all sequenced barcodes

source_name: B16-Nectin1 melanoma

extract_protocol:
Tumors were excised, minced with scissors, and incubated in RPMI with tumor digestion enzymes (Miltenyi tumor dissociation kit, Cat. no. 130-096-730) for 30 minutes at 37°C. Tumors were filtered through a 40µM strainer and cells were resuspended in FACS buffer (PBS with 2% FBS). Cells were counted with a hemocytometer and equal portions of cells from each mouse in a sample group were pooled before staining with anti-CD45-FITC (Biolegend clone 30-F11) and ZombieNIR (Biolegend #432105). Cells were sorted for ZombieNIR- CD45+ events into collection buffer (RPMI 1640, 25mM HEPES, 10% FBS) on a BD FACS Aria II at the Dana-Farber Flow Sorting Core. Sorted cells were washed one time with 5 mL of PBS + 0.05% ultrapure BSA, counted via hemocytometer, and resuspended to a concentration of 1,000 cells per microliter.
Library preparation was performed with the Chromium Single Cell 5’ Library and Gel Bead Kit (Part Number 1000006)

treatment_protocol: B16-Nectin1 tumors were treated intratumorally starting at day seven every three days for total of four injections of either PBS, d106S, or d106S-IL12. At day 10, blocking antibodies against either TNFα, IL-1β, or IL-6R (100µg per injection) were injected every three days for a total of three injections (n = 5 per treatment group). Mice were sacrificed on day 16 (PBS groups) or day 17 (d106S, d106S-IL12 groups) post tumor challenge.

value: d106S-IL12 virus + anti-IL6R antibody


title: d106S-IL12-IL1b

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral d106S-Il12 virus and IL1β blockade

value: d106S-IL12 virus + anti-IL1β antibody


title: d106S-IL12-TNFa

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral d106S-Il12 virus and TNF⍺ blockade

value: d106S-IL12 virus + anti-TNF⍺ antibody


title: d106S

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral d106S virus

value: d106S virus


title: IL1b

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral IL1β blockade

value: Anti-IL1β antibody


title: 9A_M_1106


title: SKNAS N-MYC-ER MYC-ON CT72 Replicate 2

city: Rochester

first: Brian

middle: James

last: Altman

state: NY

address: 601 Elmwood Avenue Box 633

department: Biomedical Genetics

institute: University of Rochester

data_processing:
Raw reads were processed by the GRC to demultiplex, then with FASTP to trim adaptors and remove reads that were low quality or too short.
Processed reads were mapped to transcripts using Salmon 1.3.0 in mapping-based mode for paired-end samples, using a decoy-aware transcriptome built from Gencode v35 GRCh38 primary assembly genome and v35 transcriptome.  Salmon further filtered out ambiguous reads or reads that corresponded to decoy fragments.
Transcripts were collapsed to gene-level using Tximport 1.12.3 using Gencode v35 transcriptome.  Genes were annotated with symbols using the Ensembl GRCh38.101 transcriptome annotations.
Tximport normalized raw counts to Transcripts-Per-Million (TPM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text with GENEID (Column A), SYMBOL (Column B) and TPM data of samples (Columns C-AB)

source_name: neuroblastoma cancer

growth_protocol: Cells were cultured in DMEM high glucose with 10% fetal bovine serum in a 5% CO2 incubator.

extract_protocol:
RNA was extracted with the Omega Bio-Tek E.Z.N.A.® HP Total RNA Kit according to manufacturer's instructions.
mRNA library preparation with the Illumina TruSeq Stranded mRNA kit .  Libraries were sequenced on an Illumina NovaSeq 6000 as 100PE (paired-end), yielding an average of 93.1 million reads per sample (when adding together both paired ends).

value: neuroblastoma cancer

value: SKNAS

value: N-MYC-ER overexpressing

value: 4OHT (MYC-ON), dexamethasone


title: SKNAS N-MYC-ER MYC-ON CT60 Replicate 2


title: SKNAS N-MYC-ER MYC-ON CT68 Replicate 2


title: SKNAS N-MYC-ER MYC-ON CT56 Replicate 2


title: SKNAS N-MYC-ER MYC-ON CT52 Replicate 2


title: PBS

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral PBS

value: PBS


title: 9A_M_1104


title: TNFa

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral TNF⍺ blockade

value: Anti-TNF⍺ antibody


title: UTelectro (Rep3)

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-separated count file

molecule: polyA RNA

source_name: Mobilized Peripheral Blood

extract_protocol:
Total RNA was purified 24 hrs after editing using RNeasy Micro Kit (QIAGEN). DNase treatment was performed using RNase-free DNAse Set (QIAGEN), according to the manufacturer’s instructions.
RNA was quantified with Qubit 2.0 Fluorometer (Thermo Fisher) and its quality assessed by a 2100 Agilent Bioanalyser (Agilent Technologies). Minimum quality was defined as RNA integrity number (RIN) > 8. 300 ng of total RNA were used for library preparation with TruSeq Stranded mRNA (Illumina).

value: Mobilized Peripheral Blood

value: Hematopoietic Stem/Progenitor Cells

tag: replicate

value: Rep. 3

value: Mock electro


title: 9A_M_1105


title: 9A_M_111


title: UTelectro (Rep2)

value: Rep. 2


title: SKNAS N-MYC-ER MYC-ON CT64 Replicate 2


title: SKNAS N-MYC-ER MYC-ON CT44 Replicate 2


title: UTelectro (Rep1)

value: Rep. 1


title: d106S-IL12

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral d106S-Il12 virus

value: d106S-IL12 virus


title: PrimeEditing (Rep2)

value: Prime Editing


title: 9A_M_1100


title: SKNAS N-MYC-ER MYC-ON CT36 Replicate 2


title: SKNAS N-MYC-ER MYC-ON CT48 Replicate 2


title: Day1_UT (Rep2)

source_name: Cord Blood

value: Cord Blood

value: UT

tag: time

value: Day 1


title: Day1_UT (Rep3)


title: 9A_M_1103


title: PrimeEditing (Rep3)


title: 9A_M_1102


title: Day3_UT (Rep2)

value: Day 3


title: 9A_M_11


title: 9A_M_1099


title: SKNAS N-MYC-ER MYC-ON CT28 Replicate 2

value: neuroblastoma cancer

value: SKNAS


title: 9A_M_1098


title: SKNAS N-MYC-ER MYC-ON CT24 Replicate 2

value: N-MYC-ER overexpressing

value: 4OHT (MYC-ON), dexamethasone


title: 9A_M_1101


title: SKNAS N-MYC-ER MYC-OFF CT72 Replicate 2


title: 9A_M_1107


title: SKNAS N-MYC-ER MYC-ON CT40 Replicate 2


title: Day3_BE4alone (Rep3)

value: BE4max w/o sgRNA


title: Day3_ABE8alone (Rep3)

value: ABE8.20-m w/o sgRNA


title: 9A_M_1097


title: Day3_BE4alone (Rep2)

value: Hematopoietic Stem/Progenitor Cells


title: PrimeEditing (Rep1)

value: Mobilized Peripheral Blood


title: 9A_M_110


title: SKNAS N-MYC-ER MYC-ON CT32 Replicate 2


title: Day1_UT (Rep1)


title: Day3_dCas9 (Rep2)


title: 9A_M_1095


title: Day3_UT (Rep3)

value: Rep. 3


title: Day3_Utelectro (Rep3)

value: Mock electro


title: Day3_UT (Rep1)

value: Rep. 1


title: Day3_ABE8alone (Rep2)

value: Rep. 2


title: 9A_M_1094


title: Day3_ABE8alone (Rep1)


title: Day3_Cas9 (Rep1)


title: Day3_BE4alone (Rep1)


title: SKNAS N-MYC-ER MYC-OFF CT68 Replicate 2


title: 9A_M_1091


title: Day3_dCas9 (Rep3)


title: Day3_ABE8 (Rep2)


title: 9A_M_1096


title: SKNAS N-MYC-ER MYC-OFF CT60 Replicate 2


title: SKNAS N-MYC-ER MYC-OFF CT64 Replicate 2


title: 9A_M_1090


title: Day3_dCas9 (Rep1)


title: Day3_BE4 (Rep2)


title: SKNAS N-MYC-ER MYC-OFF CT40 Replicate 2


title: Day3_BE4 (Rep1)


title: SKNAS N-MYC-ER MYC-OFF CT36 Replicate 2


title: SKNAS N-MYC-ER MYC-OFF CT56 Replicate 2


title: Day3_Utelectro (Rep1)


title: Day1_Utelectro (Rep3)


title: Day1_Utelectro (Rep2)


title: 9A_M_1089


title: Day3_Utelectro (Rep2)


title: 9A_M_1093


title: SKNAS N-MYC-ER MYC-OFF CT32 Replicate 2


title: Day3_Cas9 (Rep3)


title: SKNAS N-MYC-ER MYC-OFF CT28 Replicate 2


title: SKNAS N-MYC-ER MYC-OFF CT52 Replicate 2


title: Day3_Cas9 (Rep2)


title: 9A_M_1092


title: 9A_M_1087


title: 9A_M_1086


title: Day3_ABE8 (Rep3)


title: SKNAS N-MYC-ER MYC-OFF CT44 Replicate 2


title: Day3_ABE8 (Rep1)


title: Day1_ABE8 (Rep2)


title: Day3_BE4 (Rep3)


title: Day1_ABE8 (Rep1)


title: Day1_Utelectro (Rep1)


title: 9A_M_1088


title: SKNAS N-MYC-ER MYC-OFF CT48 Replicate 2


title: Day1_BE4 (Rep1)


title: 9A_M_109


title: Day1_Cas9 (Rep3)


title: 10x, sample A2_Recovery

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
We used cellranger count pipeline (version 3.1.0) to analyze the demultiplexed FASTQ data and generated the single cell count matrix, once for each sample. We aligned the reads to a custom “pre-mRNA” reference which was generated as described by 10X Genomics based on FlyBase R6.29.
All the matrices in different batches were aggregated into a single feature-barcode matrix by Cell ranger pipeline and normalized by equalizing the read depth among libraries.
Graph-based clustering in cellranger was applied to identify cell clusters
Assembly: Drosophila, FlyBase release r6.32
Supplementary files format and content: gene2cell matrix and metadata file of cell2cluster

organism: Drosophila melanogaster

source_name: gut

growth_protocol: Oregon R flies were raised at 23C at standard lab food and conditions and 3days old females were collected for the experiment

extract_protocol:
Single-nucleus suspension was conducted as described by Li et 2022. Briefly 70 guts per sample were dissected in cold Schneider’s medium, flash-frozen and stored at -80°C. Prior to FACs sorting, samples were spined down and Schneider’s medium was exchanged with homogenization buffer (Li et 2022). Using 1ml dounce , nuclei were released by 20 loose pestle strokes and 40 tight pestle strokes while keeping samples on ice and avoiding foam. Next, nuclei were filtered through 5 ml cell strainer (40 μm), and using 40 μm Flowmi. Nuclei were centrifuged,  resuspended in PBS/BSA with 0.5% RNase inhibitor and filtered again with 40 μm Flowmi. Single nuclei were sorted using Sony SH800Z Cell Sorter and 100k nuclei per sample were collected in PBS/BSA buffer.
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1

treatment_protocol: For the Recovery sample (A2)  flies were fed with 2%DSS in standard lab food for 4 days  and then transferred to standard lab food for 2 days prior to dissection. For Homeostasis sample (A1) flies were fed with standard lab food for 6 days prior to dissection. Both feeding regimes were conducted at 29C

value: gut

value: Oregon R

tag: condition

value: Recovery


title: 9A_M_1083


title: Day1_Cas9 (Rep1)

value: Cord Blood

value: Day 1


title: Day1_Cas9 (Rep2)


title: Day1_ABE8 (Rep3)


title: Day1_BE4 (Rep2)


title: 9A_M_1084


title: SW1990 cell,NC,KMT2D [CUT&Tag]

city: Nanjing

first: Mengying

last: Xing

address: 163 Xianlin Avenue

department: The State Key Laboratory of Pharmaceutical Biotechnology

institute: Nanjing University

description: NC

data_processing:
*library strategy: CUT&Tag
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.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
Peaks were annotated by using homer's annotatePeaks.pl
Assembly: Count the results of the annotations and plot the distribution results using R.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

source_name: Pancreatic cancer

extract_protocol:
The CUT&TAG assay was performed in accordance with the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, China, TD904).
TruePrep Index Kit V4 for Illumina (Vazyme, TD204) was used for index-labeled DNA library preparation

value: Pancreatic cancer

value: Pancreatic cancer cells

value: negative control; NC

value: shRNA


title: SW1990 cell,KMT2D-KD,H3K4me1 [CUT&Tag]

value: KMT2D knowndown; KMT2D-KD


title: SW1990 cell,KMT2D-KD,H3K4me1 [ChIP-seq]

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.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
Peaks were annotated by using homer's annotatePeaks.pl
Assembly: Count the results of the annotations and plot the distribution results using R.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (#DP214)
The ChIP-Seq library was prepared using ChIP-Seq DNA sample preparation kit (NEBNext® Ultra™II DNA) according to the manufacturer’s instructions.


title: SW1990 cell,KMT2D-KD,EBF2 [CUT&Tag]


title: SW1990 cell,NC,H3K4me1 [CUT&Tag]

description: NC


title: SW1990 cell,NC,EBF2 [CUT&Tag]

description: NC


title: 9A_M_1085


title: SW1990 cell,KMT2D-KD,KMT2D [CUT&Tag]


title: SW1990 cell,KMT2D-KD,EBF2 [ChIP-seq]


title: 10x, sample A1_Homeostasis

description: 10x genomics

value: Homeostasis


title: SW1990 cell,KMT2D-KD,KMT2D [ChIP-seq]


title: SKNAS N-MYC-ER MYC-OFF CT24 Replicate 2

value: neuroblastoma cancer

value: SKNAS

value: N-MYC-ER overexpressing

value: 4OHT (MYC-ON), dexamethasone


title: 9A_M_1079


title: 9A_M_1077


title: SW1990 cell,NC,EBF2 [ChIP-seq]


title: 9A_M_1082


title: 9A_M_1081


title: 9A_M_1080


title: Day1_BE4 (Rep3)

value: Hematopoietic Stem/Progenitor Cells

value: Rep. 3


title: SW1990 cell,NC,KMT2D [ChIP-seq]


title: 9A_M_108


title: 9A_M_1074


title: 9A_M_1072


title: SW1990 cell,EBF2-OE3 [RNA-seq]

data_processing:
The raw reads were filtered by removing reads containing adapter, ploy-N and low quality reads for  ubsequent analysis. The steps of sequencing data filtering:
1) removing reads containing adapter;
2) removing reads containing ploy-N (i.e., unrecognized bases), reads with a ratio greater than 5%
3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire read);
All the downstream analyses were based on clean data with high quality
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol (Takara). A total amount of 1μg qualified RNA per sample was used as input material for the library preparation.
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China) according to the manufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500 (Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by OligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to in structions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit (Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China). The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from rawdata. HISAT2 was used to align the clean reads to the human reference genome hg38 with default parameters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DEseq/DESeq2/edgeR/DEGseq using read counts as input. The Benjamini–Hochberg multiple test correction method was enabled.

value: overexpression


title: SW1990 cell,NC,H3K4me1 [ChIP-seq]


title: IL6R

description: CD45+ cells sorted from in vivo B16-Nectin1 melanoma treated with intratumoral IL6R blockade

value: Anti-IL6R antibody


title: 9A_M_1078


title: SW1990 cell,2000uM-2 [RNA-seq]


title: 9A_M_1075


title: 9A_M_1076


title: SW1990 cell,2000uM-1 [RNA-seq]


title: 9A_M_1069


title: SW1990 cell,Input [ChIP-seq]


title: 9A_M_1073


title: SW1990 cell,Mock-1 [RNA-seq]

value: vechicle


title: SW1990 cell,OEC-2 [RNA-seq]

value: vector


title: SW1990 cell,Mock-2 [RNA-seq]


title: 9A_M_1070


title: 9A_M_1065


title: sh_ctsv1

city: shanghai

first: wen

last: zhang

address: xiangyin road

institute: naval medical university

data_processing:
HISAT2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
SAMtools tools for related file processing
Assembly: hg38
Supplementary files format and content: Xls files include count values for each Sample

source_name: liver cancer

growth_protocol: Huh7  cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, USA). 0.1-1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver cancer

value: tumor cells

value: CTSV knockdown


title: 9A_M_107


title: 9A_M_1071


title: SW1990 cell,EBF2-OE2 [RNA-seq]

value: Pancreatic cancer

value: Pancreatic cancer cells


title: 9A_M_1068


title: 9A_M_1063


title: 9A_M_1066


title: 9A_M_1064


title: sh_con3

value: WT


title: sh_con2


title: 9A_M_1062


title: sh_ctsv3


title: sh_con1


title: 9A_M_106


title: 9A_M_1061


title: 9A_M_1059


title: 9A_M_1057


title: 9A_M_1058


title: SW1990 cell,OEC-3 [RNA-seq]


title: T24, FOXF1-activated，rep2

city: Shanghai

first: Yining

last: Hao

state: Shanghai Municipality

address: No. 197 Ruijin Second Road, Huangpu District

institute: Shanghai Ruijin Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).
We aligned reads of all samples to the reference genome using Tophat2 (2.0.4) package, remaining reads (unmapped reads) were still mapped to reference genome using tophat-fusion (2.1.0), which was subsequently used to identify circRNA.
CIRCExplorer2 (2.2.6, default) and CIRI (2.0.2, default) was used to denovo assemble the mapped reads to circular RNAs at first; Then, back-spliced junction reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2 or CIRI. All samples were generated unique circular RNAs.
We normalized the back-spliced reads (support for circRNA) by read length and number of mapped reads (spliced reads per billion mapping, denoted as SRPBM), which permits quantitative comparisons between back splicing from different RNA-seq. We counted the total number of reads mapped to the reference genome in each sample and normalized the number of reads spanning the back-spliced junction to the total number of mapped reads (units in billion) and read length. The SRPBM value of each sample circRNA was calculated by the Perl script and used as the expression abundance. SRPBM = number of circular reads/number of mapped reads (units in billion)/read length
Assembly: GRCH38
Supplementary files format and content: xlsx file include count  values for each Sample

source_name: bladder

growth_protocol: the most efficient saRNA and dsControl were selected to create short hairpin RNA (shDNA) and packaged into lentivirus (Lenti-dsFOXF1-367 or Lenti-dsControl, GenePharma). Cells were infected by lentivirus at a confluence of 60%-70%, the medium was replaced 24 hours later.

extract_protocol:
Total RNA was extracted using Trizol reagent (hermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) with RIN number > 7.0.
Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Stably activation of FOXF1 cells were selected with 3 μg/ml puromycin (Beyotime, China).

value: bladder

value: bladder cancer cells


title: T24, FOXF1-activated，rep3


title: T24, Negative control，rep1

value: Negative control


title: T24, Negative control，rep2


title: 9A_M_1060


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day24, replicate 2

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

data_processing:
The sequencing reads were firstly undergone adapter removal by ‘cutadapt’. The parameters were set as ‘-n 1 -e 0.1 -O 2 -m 16’.
Customized references were used according to the sources of the CRISPR/Cas9 libraries. Alignment was conducted using bowtie2 with ‘-np 0 --n-ceil L,0,0.2 --very-sensitive’.
Read count of each sgRNA was extracted by a custom Perl script.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include sgRNA counts for each gene
Library strategy: CRISPR screen

source_name: Peripheral blood

growth_protocol: K562-Cas9 and Jurkat-Cas9 cells were cultured in1640 medium with 10% FBS and 1 μg/ml blasticidin on confluency of 0.5 million/ml in shaking incubator at 120rpm, 37°C, and with 5% CO2.

extract_protocol:
Genomic DNA harvested using DNA isolation kit (Tiangen Biotech). All of genomic DNA was used for the construction of sequencing libraries.
Library was prepared using the NEBNext Ultra II Q5 Master Mix kit (NEB). 2ug of genomic DNA was used in each 50ul PCR reaction.

value: Peripheral blood

value: Jurkat

value: T lymphoblast

value: Genome-wide knockout

value: H-mLibB CRISPR/Cas9 library


title: T24, FOXF1-activated，rep1


title: T24, Negative control，rep3


title: 9A_M_1067


title: sh_ctsv2


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day24, replicate 1


title: 9A_M_1055


title: BG4_PFF-treated_mCTXN_rep1

city: Yokohama

first: Sefan

last: Asamitsu

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Fastq files were processed for quality check and adapter trimming with the Trimgalore! (v0.6.6).
Trimmed reads were used for mapping to the mouse genome (mm10) using the STAR (v2.7.9a).
RSEM (v1.3.1) was used for obtaining read counts.
DESeq2 (v1.38.3) was used for identifying  BG4-enriched transcripts.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: cortical tissue

extract_protocol:
Primary mouse cortical neurons (mCTXN) treated with vehicle or α-Syn PFF were crosslinked on ice cold RNase free PBS by irradiation with UV light (254 nm) at 150 mJ/cm2. Cells were harvested, lysed, and precleared on DynabeadsTM Protein G (Invitrogen) for 1 hour at 4 ℃. The precleared lysates were incubated at 4°C for three hours in a protein G magnetic beads immobilized with normal rabbit IgG (for control) or BG4 with anti-DYKDDDDK tag antibody.
Purified protein-bound RNA fraction was subjected to library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). All libraries were sequenced on a NextSeq 500 sequencer (illumina).

value: cortical tissue

value: post-mitotic neurons

value: PFF

tag: rip antibody


title: BG4_PFF-treated_mCTXN_rep2


title: 9A_M_1053


title: IgG_PFF-treated_mCTXN_rep1

value: IgG


title: IgG_PFF-treated_mCTXN_rep2


title: 9A_M_1054


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day18, replicate 2


title: BG4_PBS-treated_mCTXN_rep2

value: PBS


title: 9A_M_1052


title: BG4_PBS-treated_mCTXN_rep1


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day18, replicate 1


title: IgG_PBS-treated_mCTXN_rep2


title: 9A_M_1051


title: 9A_M_1056


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day0, replicate 2


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day12, replicate 2


title: UV_PoolA

first: Seoyeon

state: California

address: 9500 Gilman Dr.

institute: University of California, San Diego

description:
Pool of 24 UV-irradiated mice
UV_barcodes.tsv.gz
UV_features.tsv.gz
UV_matrix.mtx.gz

library_source: genomic single cell

data_processing:
Fastq files were demultiplexed by adding cell barcodes to each read. Then demultiplexed reads were aligned to mm10 using Bowtie2 and sorted by read name using samtools. Pair-end reads with mapping quality lower than 30 and improperly paired or duplicated fragments were filtered out. Cells with less than 1,000 reads and a <5 transcription start stie (TSS) enrichment score were removed. After identifying initial clusters with cell-by-bin (window) matrix, peak calling was performed using MACS2 callpeak48. Gene activity was predicted by counting the reads on the gene coordinates extended to include 2kb upstream.
Assembly: mm10 GRCm38
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.

source_name: dorsal skin

extract_protocol:
Hair on mouse dorsal skin was shaved using clippers. Dorsal skin was collected and the adipose layer under the dermis was removed using a blunt scalpel. The skin was then incubated in 4 mL of prewarmed Collagenase I (20 mg/mL in DMEM/F-12) at 37°C for 1 hour. 3 mL of keratinocyte serum-free medium (Life, cat# 17005042) was added to the cell suspension. The cell suspension was filtered using 100 μM cell strainer and the tissue chunks were incubated in 2 mL of Trypsin/EDTA 0.25% solution for 10 min. The cell suspension was filtered using 40 μM cell strainer and then centrifuged for 10 min at 200 g at 4°C. The pellet was washed with PBS and centrifuged for 10min at 200 g at 4°C. The cell pellet was resuspended in 1 mL of PBS and centrifuged for 5 min at 300 g at 4°C. After cell isolation, cell pellets were resuspended in 100 uL of cold ATAC-seq resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3mM MgCl2 in water) containing 0.1% NP40, 0.1% Twwen-20, and 0.01% digitonin, and then centrifuged for 10 min at 500 g in a pre-chilled (4°C) fixed-angle centrifuge. After removing the supernatant, nuclei were resuspended in 1 mL PBS buffer and filtered through 40 μM cell strainer. GFP+ nuclei were collected using a BD FACS Aria Fusion.
Based on the collected volume from FANS, 5X Tagmentation buffer (50mM Tris pH 7.5, 25mM MgCl2, 50% DMF, 0.5% Tween 20, 0.05% Digitonin) was added to a final concentration of 1.25X. Nuclei concentration was adjusted to about 1,000 nuclei per well based on FANS estimated number of nuclei. 8 μL of nuclei were distributed into each well of a 96-well plate containing 1 μL of each ME-A or ME-B carrying barcoded transposome per well at ~1.5 μM. Tagmentation was performed at 50°C for 30 min. Following tagmentation, 10 μL of 40 μM EDTA was added and the plate was incubated at 37°C for 15 min to terminate the Tn5 reaction. After adding 10 μL of sort buffer (2 % BSA and 2 mM EDTA in PBS), all wells were pooled and centrifuged for 5 min at 500 g. Nuclei were resuspended in 1 mL of sort buffer, filtered through a 35 μm mesh cell strainer (Corning, cat #352235) and stained with 3 μM Draq7 (Abcam, cat# ab109202). 20 Draq7+ nuclei were sorted into each well of a 96-well plate containing 16.5 μL of elution buffer (2 % BSA and 10 mM Tris pH 8.0) using a BD FASC Melody. After sorting, plates were frozen at -80°C. After thawing, 2 μL of 0.2% SDS was added to each well, the plate was incubated for 7 min at 55°C, and then 2.5 μL of 10% Triton X-100 was added. For PCR amplification, 1.5 μL of 25 μM Primer i5 and 1.5 μL of 25 μM Primer i7 were added, the plate was gently vortexed, and spun down briefly. 25 μL of PCR mix (Q5 DNA polymerase (NEB cat#M0491), 2 mM dNTP, Q5 buffer and 1X GC Enhancer) were added. PCR was performed using the following protocol: 72°C 5 min, 98°C 30 sec, 17 cycles of: [98°C 10 sec, 63°C 30 sec, 72°C 30 sec], 72°C 5 min, held at 4°C. Amplified DNA libraries were pooled and purified using MinElute columns (Qiagen cat#28004) using a vacuum apparatus (Qiagen cat#19413). Size selection was performed using Ampure XP Bead (Beckman Coulter cat#A63880). Libraries were sequenced on a mid-lane output PE 150bp on a Nextseq500 sequencer (Illumina) with custom recipe for the following, read 1: [36 imaged cycles], Index 1: [8 imaged cycles, 27 dark cycles, 8 imaged cycles], Index 2: [8 imaged cycles, 21 dark cycles, 8 imaged cycles], Read 2: [36 imaged cycles].

treatment_protocol: 7-week-old Dct-rtTA; Tre-H2B-GFP mice were used in this study. For telogen samples, drinking water containing doxycycline (Alfa Aesar, Cat#J60579, 20 mg dissolved in 100 ml sterilized water) was continuously provided for 5 days. For anagen samples, chemical depilation with Nair cream was performed to stimulate the hair cycle.  Mice were shortly anesthetized using isoflurane. Before Nair application, hair on the dorsal skin was shaved using a small animal clipper, then Nair was applied onto the dorsal skin. After hair removal, the skin was gently wiped with wet tissues to prevent any cutaneous irritation by the Nair cream. After anagen initiation, drinking water containing doxycycline (20 mg dissolved in 100 ml sterilized water) was continuously provided for 5 days. For UVB irradiation, mice were provided with drinking water containing doxycycline (20 mg dissolved in 100 ml sterilized water) for 5 days and irradiated with UVB (2.2mJ/cm2) on the dorsal skin three times over one week, with a day of rest between UVB exposures.

tag: species

value: Mouse

tag: mouse strain

value: Dct-rtTA; Tre-H2B-GFP


title: V8_T1_SCL211208RS_GEX2_S3_L002

city: Portland

first: Zinab

last: Doha

state: OR

address: 2730 S MOODY AVE

institute: Oregon Health & Science University

description:
SCL211208RS_GEX2_2
10x Genomics
V8_T1_

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mammary tissue

extract_protocol:
Tissue was manually minced using scissors, followed by a 30-60 min enzymatic digestion with 2.0 mg/ml collagenase A (Roche), 1.0 mg/ml Hyaluronidase (Worthington), and 50 U/ml DNase I (Roche) in serum-free Dulbecco’s modified eagles medium (DMEM) (Invitrogen)+ Rock inhibitor at 37C using continuous stirring conditions (5ml per sample).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: mammary tissue

value: Myc;Ptenfl

value: no


title: UV_PoolB

description:
Technical replicates of pool of 24 UV-irradiated mice
UV_barcodes.tsv.gz
UV_features.tsv.gz
UV_matrix.mtx.gz


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day0, replicate 1


title: Jurkat cells, H-mLibB CRISPR/Cas9 library, day12, replicate 1


title: 9A_M_1050


title: TEL_ANA

description:
Pool of 12 Telogen mice and 8 Anagen mice
TE_barcodes.tsv.gz
TE_features.tsv.gz
TE_matrix.mtx.gz
AN_barcodes.tsv.gz
AN_features.tsv.gz
AN_matrix.mtx.gz


title: V8_T1_SCL211208RS_GEX1_S1_L001

description:
SCL211208RS_GEX1_1
10x Genomics
V8_T1_


title: 9A_M_105


title: V8_T1_SCL211208RS_GEX1_S1_L002

description:
SCL211208RS_GEX1_2
10x Genomics
V8_T1_


title: V7_T1, V7_T2, V7_T3_GEX2_Lib_RUN5_S6_L002

description:
SCL210816RS_GEX2_RUN5_2
10x Genomics
V7_T1
V7_T2
V7_T3


title: V7_T1, V7_T2, V7_T3_GEX2_Lib_RUN5_S6_L001

description:
SCL210816RS_GEX2_RUN5_1
10x Genomics
V7_T1
V7_T2
V7_T3


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day24, replicate 2

value: H-mLibA CRISPR/Cas9 library


title: 9A_M_1049


title: V7_T1, V7_T2, V7_T3_GEX1_Lib_RUN5_S5_L002

description:
SCL210816RS_GEX1_RUN5_2
10x Genomics
V7_T1
V7_T2
V7_T3


title: 9A_M_1048


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day24, replicate 1


title: IgG_PBS-treated_mCTXN_rep1


title: 9A_M_1046


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day18, replicate 2


title: V6_T1, V6_T2, V6_T3_GEX2_Lib_RUN4_S2_L002

description:
SCL210816RS_GEX2_RUN4_2
10x Genomics
V6_T1
V6_T2
V6_T3


title: V6_T1, V6_T2, V6_T3_GEX2_Lib_RUN4_S2_L001

description:
SCL210816RS_GEX2_RUN4_1
10x Genomics
V6_T1
V6_T2
V6_T3


title: V6_T1, V6_T2, V6_T3_GEX1_Lib_RUN4_S1_L001

description:
SCL210816RS_GEX1_RUN4_1
10x Genomics
V6_T1
V6_T2
V6_T3


title: 9A_M_1045


title: V8_T1_SCL211208RS_GEX2_S3_L001

description:
SCL211208RS_GEX2_1
10x Genomics
V8_T1_


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day18, replicate 1


title: V6_T1, V6_T2, V6_T3_GEX1_Lib_RUN4_S1_L002

description:
SCL210816RS_GEX1_RUN4_2
10x Genomics
V6_T1
V6_T2
V6_T3


title: 9A_M_1044


title: V5_GEX2_Lib_CD_S4_L002

description:
SCL210602RS_GEX2_CD_2
10x Genomics
V5_


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day12, replicate 2


title: 9A_M_1043


title: V5_GEX2_Lib_CD_S4_L001

description:
SCL210602RS_GEX2_CD_1
10x Genomics
V5_


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day12, replicate 1


title: V5_GEX1_Lib_CD_S3_L002

description:
SCL210602RS_GEX1_CD_2
10x Genomics
V5_


title: V7_T1, V7_T2, V7_T3_GEX1_Lib_RUN5_S5_L001

description:
SCL210816RS_GEX1_RUN5_1
10x Genomics
V7_T1
V7_T2
V7_T3


title: V5_GEX1_Lib_CD_S3_L001

description:
SCL210602RS_GEX1_CD_1
10x Genomics
V5_


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day0, replicate 1


title: 9A_M_1040


title: 9A_M_1042


title: 9A_M_1041


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day24, replicate 2

value: Brunello CRISPR/Cas9 library


title: V3_T1, V3_T2, V4_GEX1_Lib_XL_S2_L002

description:
SCL210602RS_GEX2_XL_2
10x Genomics
V3_T1
V3_T2
V3_T3
V4


title: 18009_XL_28342_2_1

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Agilent-072363 Whole Human Genome Microarray 8x60 v3 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: Matrigel organoid medium and RPMI+FBS dissociations.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: alternativ treatment of matrigel or RPMI+FBS dissociation of human Ovarian clear cell carcinoma

value: Ovarian clear cell carcinoma injection in PDX mice and following RPMI and FBS dissociation


title: 18009_O_28342_1_3

value: Ovarian clear cell carcinoma with dissociation in matrigel organoid medium


title: 18009_OL_28342_2_2

value: Ovarian clear cell carcinoma with dissociation in matrigel organoid medium and following RPMI and FBS dissociation


title: 18009_X_28342_1_2

value: Ovarian clear cell carcinoma injection in PDX mice


title: V3_T1, V3_T2, V4_GEX1_Lib_XL_S2_L001

description:
SCL210602RS_GEX2_XL_1
10x Genomics
V3_T1
V3_T2
V3_T3
V4


title: 9A_M_104


title: 18009_XO_28342_2_3

value: Ovarian clear cell carcinoma injection in PDX mice with dissociation in matrigel organoid medium


title: V3_T1, V3_T2, V4_GEX1_Lib_XL_S1_L002

description:
SCL210602RS_GEX1_XL_2
10x Genomics
V3_T1
V3_T2
V3_T3
V4


title: 9A_M_1039


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day18, replicate 2

value: Peripheral blood

value: Jurkat

value: T lymphoblast

value: Genome-wide knockout


title: 18009_L_28342_1_4

value: Ovarian clear cell carcinoma with dissociation in RPMI and FBS


title: 9A_M_1038


title: 18009_XOL_28342_2_4

value: Ovarian clear cell carcinoma injection in PDX mice with dissociation in matrigel organoid medium and following RPMI and FBS dissociation


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day18, replicate 1


title: V3_T1, V3_T2, V4_GEX1_Lib_XL_S1_L001

description:
SCL210602RS_GEX1_XL_1
10x Genomics
V3_T1
V3_T2
V3_T3
V4


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day24, replicate 1


title: Jurkat cells, H-mLibA CRISPR/Cas9 library, day0, replicate 2


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day12, replicate 2


title: WHIM30CR7-107951

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC v.0.11.8 to identify any quality concerns with the raw data.
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
Assembly: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1).  Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary files format and content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.

organism:
Homo sapiens
Mus musculus

source_name: Basal-like triple-negative breast cancer patient-derived xenograft

growth_protocol: PDX tumors were grown orthotopically in NSG mice for 8 weeks.

extract_protocol:
Qiagen RNeasy
Library construction protocol: The RNA sample received was quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific,  Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing  library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England  Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15  minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and  adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by  PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA,  USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR  (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol:
Carboplatin Resistant:  Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.
Tamoxifen Resistant: Mice harboring PDX tumors were given tamoxifen citrate chow. These PDXs were passaged under tamoxifen citrate selection until no difference in growth rate between treated and untreated tumors was observed. These models were then termed "tamoxifen resistant."
Tamoxifen citrate: Chow was replaced with Tamoxifen citrate chow from Envigo (600mg/kg) for 2 weeks prior to tumor excision.
Estradiol Withdrawal (EWD): Ovariectomy was performed and no exogenous estrogen pellet was provided.
Estrogen pellet: Two milligram slow-release estrogen pellets were implanted subcutaneously as an exogenous source of estrogen.
Ovariectomy (OVX): Both ovaries were surgically removed from mice to withdraw the primary source of estrogen.
BYL-719: 50-100mg/kg daily
Carboplatin: 40mg/kg 3 doses spaced every 4 days

tag: biomaterial provider

value: Washington University in St. Louis

value: Carboplatin Resistant PDX

value: untreated

value: PDX mammary tumor


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day12, replicate 1


title: 9A_M_1035

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-seq2

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.


title: WHIM30CR7-107949

value: 40mg/kg carboplatin dose 4hr before study endpoint


title: 9A_M_1036


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day0, replicate 2

value: Brunello CRISPR/Cas9 library


title: WHIM30CR6-107920


title: 9A_M_1034


title: Jurkat cells, Brunelllo CRISPR/Cas9 library, day0, replicate 1


title: WHIM30CR6-107919


title: 9A_M_1033


title: K562 cells, H-mLibB CRISPR/Cas9 library, day24, replicate 2

source_name: Bone marrow

value: Bone marrow

value: Erythroleukemic cell

value: H-mLibB CRISPR/Cas9 library


title: 9A_M_1032


title: K562 cells, H-mLibB CRISPR/Cas9 library, day24, replicate 1


title: WHIM30-107947

value: PDX

value: Untreated


title: UCD52CR21-107967

value: University of Colorado Anschutz Medical Campus


title: K562 cells, H-mLibB CRISPR/Cas9 library, day18


title: 9A_M_1037


title: UCD52CR21-107966


title: 9A_M_1030


title: WHIM30CR7-107950


title: 9A_M_103


title: K562 cells, H-mLibB CRISPR/Cas9 library, day10, replicate 2


title: K562 cells, H-mLibB CRISPR/Cas9 library, day10, replicate 1


title: 9A_M_1029


title: HCI-013-107939

source_name: ER+ breast cancer patient-derived xenograft

value: Huntsman Cancer Institute

value: Estrogen pellet


title: UCD52CR21-107961


title: 9A_M_1028

source_name: C57BL/6J Male P56 Mouse Brain


title: K562 cells, H-mLibB CRISPR/Cas9 library, day4, replicate 2

value: Genome-wide knockout


title: 9A_M_1027


title: K562 cells, H-mLibB CRISPR/Cas9 library, day4, replicate 1


title: K562 cells, H-mLibB CRISPR/Cas9 library, day0


title: HCI-013-107857


title: HCI-013-107858

value: Tamoxifen citrate, Estrogen pellet


title: 9A_M_1026


title: K562 cells, H-mLibA CRISPR/Cas9 library, day24, replicate 2

value: H-mLibA CRISPR/Cas9 library


title: 9A_M_1031


title: K562 cells, H-mLibA CRISPR/Cas9 library, day24, replicate 1


title: 9A_M_1025


title: HCI-013-107806

value: OVX, EWD


title: UCD52CR21-107964

value: Carboplatin Resistant PDX


title: K562 cells, H-mLibA CRISPR/Cas9 library, day18, replicate 2


title: HCI-011-107901


title: HCI-013-107763


title: K562 cells, H-mLibA CRISPR/Cas9 library, day18, replicate 1


title: 9A_M_1022


title: K562 cells, H-mLibA CRISPR/Cas9 library, day10, replicate 2


title: HCI-011-107900


title: HCI-011-107898


title: 9A_M_1021


title: K562 cells, H-mLibA CRISPR/Cas9 library, day10, replicate 1


title: HCI-001CR7-107995

value: untreated


title: 9A_M_1020


title: K562 cells, H-mLibA CRISPR/Cas9 library, day4, replicate 2


title: HCI-001CR7-107994

value: PDX mammary tumor


title: K562 cells, H-mLibA CRISPR/Cas9 library, day4, replicate 1


title: 9A_M_102


title: K562 cells, H-mLibA CRISPR/Cas9 library, day0


title: HCI-001CR7-107993

value: 40mg/kg carboplatin dose 4hr before study endpoint


title: K562 cells, Brunelllo CRISPR/Cas9 library, day24, replicate 2

value: Brunello CRISPR/Cas9 library


title: 9A_M_1018


title: 9A_M_1024


title: HCI-001-107935


title: 9A_M_1017


title: 9A_M_1019


title: 9A_M_1023


title: 9A_M_1016


title: K562 cells, Brunelllo CRISPR/Cas9 library, day24, replicate 1

value: Bone marrow


title: K562 cells, Brunelllo CRISPR/Cas9 library, day18, replicate 2

value: Erythroleukemic cell


title: 9A_M_1015


title: BCM-5097-107822-lungmet

source_name: ER+ breast cancer patient-derived xenograft lung metastasis

value: Baylor College of Medicine

value: PDX lung met


title: BCM-5097-107769-lungmet

value: PDX


title: 9A_M_1014


title: K562 cells, Brunelllo CRISPR/Cas9 library, day10, replicate 2


title: BCM-3887-107696

value: Untreated


title: BCM-5097-107568


title: 9A_M_1013


title: K562 cells, Brunelllo CRISPR/Cas9 library, day10, replicate 1


title: BCM-2277-107573-lungmet

source_name: Basal-like triple-negative breast cancer patient-derived xenograft lung metastasis


title: 9A_M_1010


title: HCI-001CR7-107992

value: Huntsman Cancer Institute


title: BMDM, old, bio rep 6

city: Houston

first: Wen

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
The raw sequencing (fastq) files were merged from four lanes to one file (fastq) per sample
The merged sequencing (fastq) files were examined with FastQC software
The merged sequencing (fastq) files were mapped to the mouse genome using the Spliced Transcripts Alignment to a Reference (STAR) software as BAM files
The alignment (BAM) files from all samples were quantified into featureCounts.txt file using featureCounts software
Assembly: mm10
Supplementary files format and content: Quantified feature counts of alignment files from all samples.

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow cells were cultured in Dulbecco’s modified Eagle medium (DMEM) with 10% FBS, 1% P/S, 1% 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 1% GlutaMAX (ThermoFisher), and 20 ng/mL macrophage colony-stimulating factor (M-CSF) (PeproTech, 315-02). Fresh medium with M-CSF was supplied on day 3 and day 5. Cells were ready for downstream experiments on day 7.

extract_protocol:
Total RNA was isolated from BMDMs from young and old animals by using TRIzol (Invitrogen, 15596026).
The library was prepared with an Illumina TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2001) following the kit provided protocol.

value: Bone marrow derived macrophage

value: 12 months


title: BMDM, old, bio rep 5


title: BCM-5097-107931

value: Estrogen pellet


title: K562 cells, Brunelllo CRISPR/Cas9 library, day4, replicate 1

value: Genome-wide knockout


title: BCM-2277-107573


title: BCM-2147CR2-107842

value: Carboplatin


title: 9A_M_1009


title: K562 cells, Brunelllo CRISPR/Cas9 library, day18, replicate 1


title: K562 cells, Brunelllo CRISPR/Cas9 library, day0, replicate 2


title: 9A_M_101


title: K562 cells, Brunelllo CRISPR/Cas9 library, day0, replicate 1


title: 9A_M_1008


title: BMDM, old, bio rep 3


title: BMDM, old, bio rep 4


title: BCM-2147CR2-107841

value: Carboplatin Resistant PDX


title: 9A_M_1011


title: BCM-2147-107848-livermet

source_name: Basal-like triple-negative breast cancer patient-derived xenograft liver metastasis

value: PDX liver met


title: K562 cells, Brunelllo CRISPR/Cas9 library, day4, replicate 2


title: BCM-2147-107745-lungmet


title: BMDM, old, bio rep 1


title: 9A_M_1006


title: 293T_150DFO_POLII

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format. bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
To compare changes in H3K9me2 occupancy between the control and DFO treated conditions (for *.ISPTZ.bw files), input samples for each respective condition were subtracted using Deeptools (v2) bamCompare. Negative values corresponding to genomic regions with greater reads in the input file were removed from further analysis by converting all negative values to 0. The log2FC between the H3K9me2 Control and DFO samples were calculated using bamCompare with a pseudocount of 1 and corresponding Bigwig files were generated. Analysis of changes in H3K9me2 occupancy were restricted to promoter and enhancer regions within +/- 5kb of TSS for genes with called POLII peaks using the DeepTools suite.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, and 1mM NaPyr. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were harvested and washed twice with ice-cold PBS and then fixed with paraformaldehyde (1% final) for 10 min at RT. Afterwards, the paraformaldehyde solution was quenched with 2.5 M (1/20) glycine, and then, cell pellets were washed twice with PBS. Sonication: The cell pellets were resuspended with lysis buffer 1 (50 mM HEPES, pH = 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, 1X protease inhibitors) and then incubated on nutator at 4 °C for 10 min. Afterwards, cell pellets were centrifuged at 500 g for 5 min and discarded supernatant. Then, cell pellets were washed with lysis buffer 2 (10 mM Tris-HCl, pH = 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 X protease inhibitors) and resuspended with lysis buffer 3 (10 mM Tris-HCl, pH = 8.0, 1 mM EDTA, 0.1% SDS, 1 X protease inhibitors). The final volume was adjusted to be 10 times the size of each cell pellet with lysis buffer 3. Sonication was performed with 1-ml Covaris tubes which were set to 10% duty factor, 175 peak intensity power, and 200 cycles per burst for 60–1200 s. Ten percent of 10X ChIP dilution buffer (10% Triton x-100, 1 M NaCl, 1% Na-Deoxycholate, 5% N-Lauroylsarcosine, 5 mM EGTA) was added to the lysate, and samples were centrifuged at maximum speed for 15 min at 4 °C to pellet debris. Immunoprecipitation: Antibody was added (~ 10 μg per purified antibody or 40 μl of anti-sera) to each sample. After incubation at 4 °C on nutator overnight, 100 μl Protein A/G Agarose beads were added for each sample for 2 h. The agarose beads were washed 4 times with RIPA buffer (50 mM HEPES, pH = 7.5, 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate), followed by once with ice-cold TE buffer (with 50 mM NaCl). After removing the residual buffer, the DNA for each IP sample was eluted with elution buffer (50 mM Tris-HCl, pH = 8.0, 10 mM EDTA, 1.0% SDS) and reverse cross-linked at 65 °C oven for 6–15 h, followed by protease K digestion at 55 °C for 2 h. The genomic DNA fragments were then further purified with Qiagen DNA purification kit (Cat. No. 28104)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. 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.

treatment_protocol: Vehicle (H2O) or 150uM DFO for 12 hours

value: Human embryonic kidney

tag: chip antibody

value: PolII

value: 150uM DFO


title: BCM-2147-107745

value: PDX mammary tumor


title: 293T_150DFO_Input


title: 9A_M_1005

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: 293T_150DFO_H3K9me2

description: logFC.150DFOoverControl.H3K9me2.ISPTZ.bw


title: BMDM, young, bio rep 6

value: 8 weeks


title: 293T_Control_H3K9me2

value: vehicle


title: 293T_Control_POLII


title: 9A_M_1004


title: BMDM, young, bio rep 5


title: BCM-2147-107741-lungmet

value: Baylor College of Medicine

value: PDX lung met


title: BCM-2147-107744

value: PDX

value: Untreated


title: BCM-2147-107744-lungmet


title: 9A_M_1007


title: YX968_30nM  Rep 3

city: Gainesville

first: Daiqing

last: Liao

state: Florida

address: 2033 Mowry Road

department: Anatomy and Cell Biology

institute: University of Florida

data_processing:
Raw reads were trimmed by trimmomatic
Alignment was performed by using HISAT2 software
The gene expression count data were extracted using the HTseq software
The raw count data were normalized to cpm (counts per million reads)
Assembly: grch38
Supplementary files format and content: count_ori.csv: csv file containing raw count data
Supplementary files format and content: cpm_ori.csv: csv file containing normalized data (count per million reads)

extract_protocol:
Qiagen Rneasy mini kit
Ilillumina Stranded mRNA Prep

value: Triple-negative breast cancer


title: BMDM, old, bio rep 2

value: Bone marrow derived macrophage

value: 12 months


title: BMDM, young, bio rep 3


title: BCM-2147-107741


title: BMDM, young, bio rep 2


title: BCM-15057EI4-107877

value: Estrogen independent PDX

value: OVX, EWD


title: YX968_30nM  Rep 2


title: YX968_30nM  Rep 1


title: BMDM, young, bio rep 1


title: BCM-15057EI3-107630


title: 9A_M_1001

last: Ecker


title: 9A_M_1000


title: 9A_M_10


title: 9A_M_1002


title: YX968_3nM  Rep 2


title: YX968_3nM  Rep 3


title: 3299a_3301b

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

data_processing:
Single cell RNAseq data basecalling, demultiplexing, alignment to mouse genome and transcript quantification were performed by Cell Ranger v6.0.2  (10x Genomics)
Genome_build: GRCm38 (mm10) mouse genome assembly
Supplementary_files_format_and_content: csv files containing raw count matrices

source_name: PDGFB-driven Glioma cells

extract_protocol:
Sorted cells were washed twice in PBS-EDTA to reduce ambient RNA contamination and avoid cell aggregation. A total of 4000 cells was used for emulsion partitioning using Chromium Controller (10x Genomics).
Sequencing libraries were generated using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Dual Index (10x Genomics).

value: Glioma cells


title: 3298a_3301a


title: 9A_M_1003

city: La Jolla


title: BCM-15057EI3-107640


title: 293T_Control_Input


title: 9A_M_100


title: BCM-15057-107968

value: Estrogen pellet


title: 9A_M_1


title: BMDM, young, bio rep 4


title: YX968_3nM  Rep 1


title: 3229B PDGFB_pos

data_processing:
Base calling was performed with default Illumina NextSeq500 workflow
Bulk RNAseq data was aligned to GRCm38 (mm10) mouse genome assembly using STAR v2.7.5c
Transcript quantification was performed using RSEM v1.3.1
Genome_build: GRCm38 (mm10) mouse genome assembly
Supplementary_files_format_and_content: mouseGliomasPDGFB_expected_counts.csv

source_name: Glioma cells

extract_protocol:
Brains were explanted and tumors microdissected under epifluorescence microscope. Cells were and sorted by FACS to separate glioma fluorescent cells from surrounding, non-fluorescent cells. RNA was harvested using MinElute RNA micro kit (Qiagen).
Sequencing libraries were generated using CORALL Total RNA-Seq Library Prep Kit (Lexogen) on PolyA+ RNA.

tag: time (survival after transduction)

value: 34 days

tag: mouse exhibiting symptoms on the day of sample collection

value: FALSE


title: BCM-15057-107957

tag: tissue


title: DMSO Control  Rep 3

tag: cell type

value: DMSO


title: 3229B PDGFB_neg

source_name: Glioma-surrounding cells

value: Glioma-surrounding cells


title: 9A_M_0


title: BCM-15034TamR3-107924

value: Tamoxifen Resistant PDX

tag: treatment

value: Tamoxifen citrate, Estrogen pellet

value: PDX mammary tumor


title: Myc-4

city: Jinan

first: Jinyuan

last: Liang

address: wenhua road

institute: Shandong university

data_processing:
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results
Assembly: mm10
Supplementary files format and content: FPKM values were provided in a tabular format.

source_name: BDL-treated endothelial Myc overexpression mice

extract_protocol:
Total RNA was extracted from the liver samples using the TRlzol Reagent (Lifetechnologies). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer's protocols.

value: liver

tag: genotype

value: LSEC Myc overexpression

value: bile duct ligation surgery


title: DMSO Control  Rep 2

value: Triple-negative breast cancer


title: 3228D PDGFB_neg

value: 33 days


title: BCM-15034TamR3-107922

value: Baylor College of Medicine


title: DMSO Control Rep 1


title: 3228D PDGFB_pos


title: BCM-15034-107894

value: PDX


title: 3228B PDGFB_neg


title: HCT116, Input

city: Guangzhou

first: Youwei

last: Huang

address: West Huangpu Avenue no.601

institute: Jinan University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Large intestine, Colon

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented by partial digestion with Micrococcal Nuclease (Cell Signaling Technology).
ChIP-seq libraries were prepared using the QIAseq Ultralow Input Library Kit (QIAGEN). 10 ng of DNA was used as starting material for Input and IP samples. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Large intestine, Colon

value: Colorectal cancer cell


title: BCM-0132-107564

value: Untreated


title: WHIM30-107662

value: Washington University in St. Louis


title: 3228B PDGFB_pos

value: Glioma cells

value: FALSE


title: Myc-3


title: 3228A PDGFB_neg

value: Glioma-surrounding cells


title: Ctrl-3

source_name: BDL-treated wild typee mice

value: WT


title: Myc-2


title: HCT116, VCP, Abcam

value: VCP (Abcam, #ab109240)


title: Myc-1


title: 3145A PDGFB_neg

value: 35 days

value: TRUE


title: ZW5728_23

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description: dataTPMbulk.csv

data_processing:
The raw data was processed with cellranger.
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor and B cell receptor VDJ analysis: Cellranger
VDJ of T cells and B cells were infered with cellranger vdj pipeline to get TCR and BCR contig annotations.
Genome_build: hg19
Supplementary_files_format_and_content: expression_data; VDJ

extract_protocol: Libraries of gene expression (BMMNCs and Lineage-CD34+HSPCs) for healthy donors 1-4, and UPNs 6,11,1,10, and 13 were generated using Genomics Chromium Single Cell 3' Solution Kit from 10XGenomics. Libraries of gene expression (BMMNCs and Lineage-CD34+HSPCs) and TCR/BCR sequencing for UPNs 14-17 were generated using Genomics Chromium Single Cell 5' Solution Kit from 10XGenomics. Libraries of gene expression of four human leukemic cell lines (U937, Raji, Jurkat, and THP1) with UBA1 knockdown were generated using Illumina NovaSeq.

tag: genotype/variation

value: knockdown


title: Ctrl-2

value: liver

value: bile duct ligation surgery


title: Ctrl-4


title: Ctrl-1


title: 3145A PDGFB_pos


title: WHIM30-107661

value: PDX mammary tumor


title: WHIM30-107660

value: 50mg/kg byl-719 gavage


title: ZW5728_21

description: dataTPMbulk.csv


title: HCT116, Flag, CST


title: WHIM30CR-107502

value: Carboplatin Resistant PDX


title: 3109D PDGFB_neg

value: 50 days


title: 3109D PDGFB_pos


title: 3228A PDGFB_pos

value: 33 days


title: ZW5728_20

description: dataTPMbulk.csv

value: Control


title: WHIM30-107659

value: Washington University in St. Louis

value: PDX


title: WHIM30-107658

value: 100mg/kg byl-719 gavage


title: 3108D PDGFB_neg

value: Glioma-surrounding cells

value: 43 days


title: ZW5728_18

description: dataTPMbulk.csv

source_name: Jurkat

value: Jurkat


title: ZW5728_19

description: dataTPMbulk.csv


title: UCD52CR-107591

value: University of Colorado Anschutz Medical Campus

value: Carboplatin 40mg/kg 3x 2wk before study endpoint


title: Mouse #L2, APP/PSEN1, synaptosome

city: Seattle

first: Paul

middle: Nils

last: Valdmanis

state: WA

address: 1705 NE PACIFIC ST.

department: Department of Medicine: Division of Medical Genetics

institute: University of Washington

data_processing:
Sequencing was outsourced to GeneWiz/Azenta with 2x150bp reads and 30x coverage. GeneWiz/Azenta provided us with paired .fastq files separated by each barcoded sample with the illumina adaptors trimmed.
paired .fastq files were aligned to the Gencode version M31 mus musculus transcriptome using RNA-Star (default parameters) and samtools was used to produce sample .bam and .bai files
For differential expression analysis, reads were mapped and counted using salmon (default settings). Resulting files were imported and analyzed in R using the DESeq2 package.
Assembly: Gencode mouse transcrips version M31
Supplementary files format and content: .sf (salmon) transcript quantification

source_name: brain (frontal cortex)

extract_protocol:
First, synaptosomes were fractionated from frontal cortex brain tissue according to the Whittaker et al. (1964) protocol. Approximately 300 mg of brain tissue was homogenized using a glass douncer in 1.5 mL of homogenization buffer: 0.32 M sucrose, 1 mM sodium bicarbonate, 1 mM magnesium chloride, 0.5 mM calcium chloride, 100 μM aurintricarboxylic acid, 24 U/mL NEB Murine RNAse inhibitor, and 0.5x Thermo HALT protease and phosphatase inhibitor cocktail. Following homogenization, 120 μl of homogenate was set aside for RNA extraction and sequencing and additional analyses. The remaining homogenate was spun down at 750 × g for 10 min at 4ºC to remove debris. Next the supernatant was centrifuged at 13,800 × g to produce a pellet of crude synaptosomes. The supernatant was collected as the cytoplasmic fraction. The crude synaptosome pellet was resuspended in 1 mL of homogenization buffer. A discontinuous sucrose gradient was prepared in a 4.2 mL ultracentrifuge tube with a 1 mL bottom layer of 1.2 M sucrose + 1 mM sodium bicarbonate, 1 mL middle layer of 1.0 M sucrose + 1 mM sodium bicarbonate, and a 1 mL top layer of 0.85 M sucrose + 1 mM sodium bicarbonate. The 1 mL of resuspended crude synaptosome was layered on top of the gradient. The samples were then spun using a swinging bucket rotor in an ultracentrifuge at 28,000 rpm (~82,000 × g). The purified synaptosomes were collected from the interface between the 1.2 M and 1.0 M layers. RNA was subsequently extracted from 500 μl of the collected synaptosomes with Trizol/chloroform.
We used the total stranded RNA with ribo-removal kit and followed the corresponding protocol from Illumina, product: 20040529; rna libraries from each sample (mouse, homogenate or synaptosome) were individually barcoded and pooled in batches of 12 (6 homogenate + 6 synaptosome)

value: brain (frontal cortex)

value: Isolated synaptosomes


title: Mouse #LR, APP/PSEN1, homogenate

value: Bulk brain homogenate


title: ZW5728_16

description: dataTPMbulk.csv

value: knockdown


title: Mouse #LR, APP/PSEN1, synaptosome


title: ZW5728_22

description: dataTPMbulk.csv


title: anti HA tag

city: Epalinges

first: Grégory

last: Verdeil

state: Vaud

address: Chemin des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: University of Lausanne

description: NFAT5 - Hatag

data_processing:
We used the nf-core/cutandrun (v3.1, CITE: doi: 10.5281/zenodo.5653535) bioinformatic pipeline for CUT&RUN analysis
Deduplication of target reads and control reads was performed by setting the --dedup_target_reads parameter to true
Target read normalization was performed using "CPM" mode with a normalisation binsize of 1 (the binsize that the reads count is calculated on)
Peak calling was performed via SEACR using internat normalization (--seacr_norm "norm") and relaxed stringency (--seacr_stringent "relaxed"). The IgG experiments were assigned as controls to the other experimental groups.
Assembly: GRCm38
Supplementary files format and content: bigWig read coverages
Library strategy: CUT&RUN

source_name: CD8 T cells

growth_protocol: Primary T cells were cultured in complete RPMI 1640 GlutaMAXTM-I.

extract_protocol:
Post antibody incubation, samples were processed following manufacturer's instruction (EpiCypher)
Libraries were prepared following the manufactures instruction (EpiCypher) with the modification of increasing the concentration of the beads to ensure smaller fragments were not lost during the purification process. Libraries were pooled and subjected to BluePeppin size selection to exclude the adapter dimers present in the libraries.

treatment_protocol: Samples were incubated with either anti-HA tag antibody or IgG control.

tag: cut&run antibody

value: anti HA tag

value: CD8 T cells

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ    NFAT5 fl/fl CD4-Cre+/-

value: 3xHA tagged NFAT5 expression


title: IgG

description: IgG control

value: IgG


title: 3108D PDGFB_pos

value: Glioma cells

value: TRUE


title: ZW5728_17

description: dataTPMbulk.csv

tag: cell line


title: UCD52CR-107532

source_name: Basal-like triple-negative breast cancer patient-derived xenograft

value: Carboplatin Resistant PDX

value: Untreated

value: PDX mammary tumor


title: UCD52-107627

value: PDX


title: 3108C PDGFB_neg

value: Glioma-surrounding cells

value: 43 days


title: Mouse #L2, APP/PSEN1, homogenate

value: brain (frontal cortex)


title: Mouse #907, APP/PSEN1, synaptosome

value: Isolated synaptosomes


title: 3108C PDGFB_pos


title: ZW5728_14

description: dataTPMbulk.csv

value: Control

value: Jurkat


title: UCD52CR-107592

value: University of Colorado Anschutz Medical Campus

value: Carboplatin 40mg/kg 3x 2wk before study endpoint


title: UCD52-100916


title: 3057E PDGFB_pos

value: 100 days


title: Mouse #907, APP/PSEN1, homogenate

value: Bulk brain homogenate


title: 3057E PDGFB_neg


title: ZW5728_13

description: dataTPMbulk.csv


title: 3054C PDGFB_neg

value: 175 days


title: ZW5728_12

description: dataTPMbulk.csv

source_name: Raji

value: knockdown

value: Raji


title: Mouse #906, APP/PSEN1, synaptosome


title: HCI-013-107415

source_name: ER+ breast cancer patient-derived xenograft

value: Huntsman Cancer Institute

value: Tamoxifen citrate, Estrogen pellet


title: HCI-013-107411

value: EWD

value: PDX mammary tumor


title: Mouse #906, APP/PSEN1, homogenate


title: 3054B PDGFB_neg

value: Glioma-surrounding cells

value: TRUE


title: ZW5728_15

description: dataTPMbulk.csv


title: Mouse #889, Wildtype, synaptosome

value: brain (frontal cortex)

value: WT


title: HCI-011-107522

value: PDX

value: Estrogen pellet


title: HCI-013-102249


title: Mouse #889, Wildtype, homogenate


title: HCI-011-107518


title: ZW5728_7

description: dataTPMbulk.csv

value: Control


title: UCD52-100398

value: University of Colorado Anschutz Medical Campus

value: Untreated


title: HCI-011-107333


title: 3054B PDGFB_pos

value: Glioma cells


title: 3054A PDGFB_pos

value: 120 days


title: HCI-011-107176


title: 3054A PDGFB_neg


title: ZW5728_9

description: dataTPMbulk.csv

value: knockdown


title: Mouse #859, APP/PSEN1, synaptosome

value: Isolated synaptosomes


title: Mouse #871, APP/PSEN1, synaptosome


title: ZW5728_5

description: dataTPMbulk.csv


title: Cpt1biKO_3_4weeks_after_TAM

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38.p5) using STAR 2.6.1d with the parameter ““--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000” (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.3 from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10 / GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited matrix with DESeq differential expression analysis and DESeq normalized gene counts.

source_name: Adult CM

extract_protocol:
RNA was extracted from isolated adult CMs using the Direct-zol Total Kit (Zymo Research) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified LabChip Gx Touch 24 (Perkin Elmer). 200ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech) following the manufactures instructions.

treatment_protocol: Tamoxifen (TAM) was administered intraperitoneally at 75mg/kg body weight daily for 10 days for both Ctrl and Cpt1biKO mice. Mice were sacrified around 4 weeks after last dose of TAM.

tag: strain

tag: age

value: 13-15 weeks

value: cardiomyocyte


title: HCI-011-107171

value: Huntsman Cancer Institute

value: EWD


title: ZW5728_11

description: dataTPMbulk.csv

value: Raji


title: Cpt1biKO_2_4weeks_after_TAM


title: 3054C PDGFB_pos

value: 175 days

value: TRUE


title: Mouse #859, APP/PSEN1, homogenate

value: brain (frontal cortex)

value: Bulk brain homogenate


title: ZW5728_10

description: dataTPMbulk.csv


title: Mouse #787, Wildtype, synaptosome

value: WT


title: ZW5728_3

description: dataTPMbulk.csv


title: ZW5728_6

description: dataTPMbulk.csv


title: ZW5728_4

description: dataTPMbulk.csv


title: Mouse #787, Wildtype, homogenate


title: Ctrl_3_4weeks_after_TAM

value: control


title: Cpt1biKO_1_4weeks_after_TAM


title: HCI-011-107170

value: PDX

value: PDX mammary tumor


title: ZW5728_2

description: dataTPMbulk.csv

value: Control


title: Ctrl_2_4weeks_after_TAM


title: HCI-001CR-107552

value: Carboplatin Resistant PDX

value: Carboplatin


title: ZW5728_1

description: dataTPMbulk.csv


title: HCI-001-100097

value: Untreated


title: Mouse #786, Wildtype, homogenate


title: Ctrl_1_4weeks_after_TAM

value: 13-15 weeks


title: UPN17_BM_BCR

source_name: Human Bone Marrow

tag: Sex

value: Male

tag: subject id/status

tag: tissue/cell type

value: Human Bone Marrow


title: Mouse #785, APP/PSEN1, synaptosome

value: Isolated synaptosomes


title: Mouse #785, APP/PSEN1, homogenate


title: Cpt1bcKO_3

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38.p5) using STAR 2.5.4b with the parameter ““--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000” (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10 / GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited matrix with DESeq differential expression analysis and DESeq normalized gene counts.

value: 8-12 weeks

value: cardiomyocyte


title: BCM-5097-107567

value: Baylor College of Medicine

value: Estrogen pellet


title: UPN15_BM_BCR


title: BCM-7482-107504


title: HCI-001CR-107553

value: Huntsman Cancer Institute


title: Mouse #786, Wildtype, synaptosome

value: brain (frontal cortex)

value: WT


title: BCM-15034-107510

value: PDX


title: Cpt1bcKO_2


title: UPN14_BM_BCR


title: Mouse #784, APP/PSEN1, synaptosome


title: Mouse #784, APP/PSEN1, homogenate

value: Bulk brain homogenate


title: CtrlCre_3


title: BCM-15057-107336

value: PDX mammary tumor


title: Cpt1bcKO_1


title: Mouse #3, Wildtype, synaptosome


title: UPN16_BM_TCR


title: CtrlCre_2


title: Mouse #3, Wildtype, homogenate


title: UPN15_BM_TCR


title: CtrlCre_1


title: Mouse #2, Wildtype, synaptosome


title: UPN14_BM_TCR


title: ChIP-Cpt1bcKO_2

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus theEnsembl mouse genome version mm10 (GRCm38.p5) using STAR 2.6.1d with the parameters ““--outFilterMismatchNoverLmax 0.1 --outMultimapperOrder Random --outSAMmultNmax 1 --outFilterMultimapNmax 1 --alignEndsType EndToEnd --alignIntronMax 1” (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining only unique alignments.
Reads were deduplicated using Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
The MUSIC peakcaller (version from Dec. 2015) was employed in punctate mode to identify enriched regions when comparing the respective ChIP to input samples (Harmanci et al., MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
To enable comparison of peaks in different samples, the resulting lists of significant peaks were overlapped and unified to represent identical regions. Sample counts for union peaks were produced using bigWigAverageOverBed (UCSC Toolkit).
Data was corrected for the background signal by subtracting coverage of the Input sample from coverage of the ChIP sample after application of a smoothing window of 100nt length using wiggletools (Zerbino DR et al., WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis).
DESeq2 1.26.0 was used to normalize the resulting matrix of union peak scores to compensate for differences in sequencing depth, library composition, and pull-down efficiency (Anders et al., Differential expression analysis for sequence count data).
Union peaks were annotated with the promoter of the nearest  gene in range (TSS +- 5000 nt) using reference data of GENCODE vM15.
Genome_build: mm10 / GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited matrix with DESeq differential analysis and DESeq normalized union peak counts.

extract_protocol:
The ChIP samples were prepared from FACS-sorted adult CM nuclei with truChIP Chromatin Shearing Kit (Covaris); then immunoprecipitation was performed with H3K4me3 antibody (Diagenode). Precipitated DNA samples were purified by MinElute PCR Purification Kit (Qiagen) and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).
0.5-10ng of DNA was used as input for TruSeq ChIP Library Preparation Kit (Illumina) with following modifications. Instead of gel-based size selection before final PCR step, libraries were size selected by SPRI-bead based approach after final PCR with 18 cycles.

tag: chip target


title: UPN16_BM_BCR


title: UPN16_BM_geneexpression


title: ChIP-Cpt1bcKO_3


title: UPN15_BM_geneexpression


title: ChIP-CtrlCre_3


title: UPN17_BM_geneexpression


title: Mouse #2, Wildtype, homogenate


title: Mouse #1, Wildtype, synaptosome


title: UPN13_BM_geneexpression


title: UPN17_BM_TCR


title: UPN10_BM_geneexpression


title: mouse_primary tumor 1

city: Vancouver

first: Yemin

last: Wang

state: BC

address: 2660 Oak Street

country: Canada

institute: University of British Columbia

data_processing:
Read quality was checked for each sample using FastQC v0.11.5.
Trimmed sequencing reads were aligned to the GRCM38/mm10 genome using STAR (v2.5.3a).
Counts were generated from the .bam files outputted from STAR using HTSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: oviduct

growth_protocol: primary normal and tumor tissues from mice

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads for cDNA synthesis using random hexamer primers
Library preparation was conducted using Illumina PE150 kits following the manufacutrer' instruction.

treatment_protocol: no treatment.

value: oviduct


title: Input-Cpt1bcKO_3

value: Input


title: Input-Cpt1bcKO_2


title: ChIP-Cpt1bcKO_1


title: Mouse #1, Wildtype, homogenate


title: ChIP-CtrlCre_2


title: UPN14_BM_geneexpression


title: mouse_oviduct 5


title: ChIP-CtrlCre_1


title: mouse_primary tumor 2


title: UPN1_BM_geneexpression


title: Input-Cpt1bcKO_1


title: mouse_oviduct 4


title: UPN11_BM_geneexpression


title: Input-CtrlCre_3


title: mouse_primary tumor 3


title: mouse_primary tumor 4


title: Input-CtrlCre_1


title: mouse_oviduct 3


title: Input-CtrlCre_2


title: HD4_BM_geneexpression


title: Gastrocnemius muscle, myonectin-KO 4

city: Nagoya

first: Koji

last: Ohashi

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore! (ver.0.6.4).
Trimmed sequence reads were mapped to GRCm39 GENCODE vM30 using STAR (2.7.3a).
Read count extraction was performed using HTSeq-count (ver.0.11.2) .
Assembly: GRCm39 GENCODE vM30
Supplementary files format and content: tab-delimited text file includes read count values for each Sample

source_name: Gastrocnemius muscle

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen), and isolated total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Gastrocnemius muscle

value: myonectin knockout

value: Sciatic nerve denervation


title: mouse_oviduct 1


title: mouse_oviduct 2


title: HZ62_silique_rep2

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

data_processing:
Adaptors and low-quality reads were first trimmed using Fastp with default parameters
Clean reads were mapped to the Brassica napus ZS11 genome（Chen et al., 2021）using Hisat2 with default parameters
SAMtools with parameters “-q 30 -f 2” was used to remove the low mapping quality reads，then GATK MarkDuplicates was used to rm duplicated reads
Reads numbers per gene were counted using FeatureCounts
The trimmed mean of M-values (TMM) method of EdgeR was used to normalization reads counts per gene
Assembly: Brassica napus ZS11 （Chen et al., 2021）
Supplementary files format and content: tab-delimited text files include TMM values for each sample
Supplementary files format and content: tab-delimited text files include reads numbers per gene for each sample

organism: Brassica napus

source_name: silique

extract_protocol:
Total RNA was isolated from the tissues (seedling, flower bud, silique) using the RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions. About 2ug RNA was used for library construction using Illumina TruSeq RNA Kit according to the manufacturer’s instruction.
About 2ug RNA was used for library construction using Illumina TruSeq RNA Kit according to the manufacturer’s instruction.

treatment_protocol: a day/night cycle of 16h/8h and a temperature of 22/18℃

value: silique


title: aPL 7

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

description:
smallRNA 50nts
ACL7_35468_ATGTCA

data_processing:
FASTQC V0.11.4 was used for raw data quality control
Rsubred R package was used for alignment and counting step of raw counts
Statistical language "R" (R version 3.6.2 (2019-12-12), Copyright The R Foundation for Statistical Computing), and the libraries developed for the miRNAseq analysis in the Bioconductor Projec was used for the rest of steps of the previous pipeline
Homo sapiens GRCh38, realease 86, (downloaded from Ensembl) was used for maping step
Assembly: Homo sapiens GRCh38, realease 86
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: sEVs from plasma

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
miRNA libraries for miRNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: sEVs from plasma

tag: subject status

value: aPL patient


title: Gastrocnemius muscle, myonectin-KO 3


title: aPL 8

description:
smallRNA 50nts
ACL8_35468_CCGTCC


title: aPL 6

description:
smallRNA 50nts
ACL6_35468_AGTTCC


title: aPL 5

description:
smallRNA 50nts
ACL5_35468_AGTCAA


title: HD2_BM_geneexpression

value: Male

value: Human Bone Marrow


title: HZ62_silique_rep1

value: a day/night cycle of 16h/8h and a temperature of 22/18℃


title: aPL 4

description:
smallRNA 50nts
ACL4_35468_CTTGTA


title: UPN17_CD34_geneexpression

source_name: FACS sorted Linjeage-CD34+ bone marrow

value: FACS sorted Linjeage-CD34+ bone marrow


title: HZ62_flower_rep2

source_name: flower bug

value: flower bug

value: <2 mm


title: UPN16_CD34_geneexpression


title: Gastrocnemius muscle, myonectin-KO 1


title: HZ62_seedling_rep2

source_name: seedling

value: seedling

value: 2 weeks

value: WT


title: Gastrocnemius muscle, myonectin-KO 2


title: UPN6_BM_geneexpression


title: aPL 3

description:
smallRNA 50nts
ACL3_35468_GGCTAC


title: UPN14_CD34_geneexpression


title: HZ62_flower_rep1


title: HD3_BM_geneexpression


title: aPL 2

description:
smallRNA 50nts
ACL2_35468_TAGCTT


title: UPN15_CD34_geneexpression


title: UPN13_CD34_geneexpression


title: Gastrocnemius muscle, WT 4


title: HD1_BM_geneexpression


title: HZ62_seedling_rep1


title: Mouse #871, APP/PSEN1, homogenate

value: brain (frontal cortex)

value: Bulk brain homogenate


title: aPL 1

description:
smallRNA 50nts
ACL1_35468_GATCAG


title: UPN10_CD34_geneexpression