title: E16.5, p18mKO2+, rep3

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
The adapter sequences were trimmed by cutadapt v3.4
Paired-end reads were aligned to the mouse transcriptome GRCm38 (Ensembl release 100) by STAR v2.7.2b.
The quantity of aligned read count was estimated by RSEM v1.2.31.
Assembly: mm10
Supplementary files format and content: tab separated RSEM results

source_name: dorsal cortex

growth_protocol: Normal development

extract_protocol:
The tissue fragment was extracted from ventrical zone in the dorsal cortex by LMD cut.
Libraries were generated using the NEXTflex™ Rapid Directional RNA-Seq Kit (NOVA-5198-10) with RNA-Seq Barcodes 1-24 beads.

treatment_protocol: The specific gene expression was induced by Cre-LoxP recombination using tamoxifen applied by intraperitoneal injection.

value: dorsal cortex

tag: Stage

value: p18mKO2 over-expression

value: Tamoxifen administration


title: DNMT1/L1TD1-1_repeat

status: Public on Dec 25 2024

type: SRA

city: Vienna

first: Christian

last: Seiser

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description:
sample name:
52683

library_source: transcriptomic

data_processing:
SCS: PN:HiSeq Control Software,VN:2.2.58,Controlling software on instrument
basecalling: PN:RTA,VN:1.18.64.0,Basecalling Package
bcl2fastq: PN:bcl2fastq,VN:2.16.0,bcl2fastq
fastq2bam: PN:fastq2bam,VN:0.3,conversion to unaligned bam files
BamIndexDecoder: PN:BamIndexDecoder,VN:V1.16-1-g590b59e-dirty,demultiplexging
bam2fastq: PN:samtools,VN:1.3.1,conversion to fastq
zcat: PN:zcat,VN:unknown,merging of fastq files of the same sampleid
cutadapt: PN:cutadapt,VN:v1.4.2,adapter trimming,--match-read-wildcards -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
bowtie2: PN:bowtie2,VN:2.1.0 ,rRNA removal by alignment to rDNA,--very-sensitive-local,KY962518.1, NR_023363.1 and the ERCC.fa
star: PN:STAR,VN:v2.4.2a,mRNA alignment,--outSAMstrandField None --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverLmax 0.1 --outFilterMismatchNmax 10 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterMatchNmin 30 --chimSegmentMin 15 --quantMode TranscriptomeSAM --chimJunctionOverhangMin 15 --twopassMode Basic --outSAMtype SAM --outSAMattributes All --outReadsUnmapped Fastx intronMotif --alignIntronMax 200000  --outSJfilterIntronMaxVsReadN 10000 20000 30000 50000 --outSJfilterOverhangMin 20 12 12 12 --outFilterType BySJout --alignMatesGapMax 0  --outFilterMultimapNmax 20,
htseq: PN:htseq-count ,VN:0.6.0,read counting,--mode union --stranded reverse
combine: PN:combine.py,VN:0.3.0,combines counts to table
repenrich: PN:RepEnrich,VN:commit 0e9228149b2aff06874ed7ff0c8836aefa864c9e,repeat enrichment. Citation: Criscione, S.W., Zhang, Y., Thompson, W. et al. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics 15, 583 (2014). https://doi.org/10.1186/1471-2164-15-583
diff: PN:deseq2,VN:1.10.1,differential expression
transcriptome annotation: ENSEMBL Homo_sapiens.GRCh38.78
Genome_build: GRCh38
Supplementary_files_format_and_content: *htseq.counts.tab: counts of reads per gene, combined reads from both sequencing runs
Supplementary_files_format_and_content: repeats_counts.tab: containing the reads aligned against repeats with RepEnrich also the combined reads from both sequencing runs
Supplementary_files_format_and_content: DNMT1_vs_Control.tab: differential expression of genes DNMT1 vs Control
Supplementary_files_format_and_content: DNMT1_L1TD1_vs_Control.tab: differential expression of genes DNMT1 L1TD1 vs Control
Supplementary_files_format_and_content: DNMT1_L1TD1_vs_DNMT1.tab: differential expression of genes DNMT1 L1TD1 vs DNMT1

molecule: total RNA

organism: Homo sapiens

source_name: HAP1 cells

extract_protocol:
Total RNA was isolated following the manufacturer’s instructions (TRIzol, Invitrogen) and then used for RNA sequencing.
For transcriptome sequencing (RNA-seq) experiments, RNA was subjected to poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by reverse transcription using a NEB RNA Ultra kit and library generation using a TruSeq library generation kit (Illumina).

treatment_protocol:
HAP1 cells were cultured then harvested for RNA isolation.
HAP1 is a near-haploid cell line derived from the KBM-7 cell line. KBM-7 was found in a patient with chronic myeloid leukemia (CML). This cell line has a haploid karyotype except for chromosomes 8 and 15. It also possesses a reciprocal chromosomal translocation of Chromosomes 9 and 22 which created a Philadelphia chromosome.

tag: genotype

tag: Sex

value: male

tag: cell line

value: HAP1 cells


title: E13.5, p18mKO2+, rep3

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: DNMT1-3_repeat

description:
sample name:
52682


title: OT-1 cell, sgTnfaip3-2, co-culture with cancer cell, rep2

city: Beijing

first: Zexian (Davis)

last: Zeng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

data_processing:
RNA-Seq immune analysis pipeline (RIMA)
sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1d
Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized abundance measurements generated by DESeq2

extract_protocol:
RNA was harvested using the Rneasy mini plus kit by Qiagen. A total of 1.3 micrograms (μg) of RNA was utilized for the construction of sequencing libraries, which is a process for preparing RNA samples for next-generation sequencing.
The libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit, adhering strictly to the protocols provided by the manufacturer. This step involves converting RNA into a library of cDNA fragments with adaptors attached to each end, a prerequisite for sequencing.

tag: cell type

value: CD8+ T cell

value: Tnfaip3 knockout


title: P47L

type: RNA

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

country: USA

institute: City of Hope

description: Surgical pathology archives queried for HER2- ER+ breast cancer patients  treated with endocrine therapy, including selective estrogen receptor modulators (SERMs), selective estrogen receptor degraders (SERDs), and aromatase inhibitors (AI) following resection of the primary tumor

hyb_protocol: RNA was hybridized with codeset at 65°C for 16 hours. Samples were processed on the NanoString Prep Station and the target-probe complex was immobilized onto the analysis cartridge.

scan_protocol: Cartridges were scanned by the nCounter Digital Analyzer for digital counting of molecular barcodes corresponding to each target at 280 fields of view.

data_processing: All NanoString gene expression data analysis was performed using nSolver Analysis Software v3.0 (NanoString Technologies, Seattle, WA). Raw data was normalized by subtracting the mean plus one standard deviation of eight negative controls while technical variation was normalized through internal positive controls. Data was corrected for input volume via eight internal housekeeping genes using the geNorm algorithm. Clinical, tumor, and patient characteristics were analyzed in relation to recurrence status. Relative gene expression was analyzed by recurrence status. PAM50 subtype analysis was performed to identify molecular subtypes. Bioinformatics analysis was performed based on the ingenuity pathway analysis (IPA) tool (version 73620684, http://www.ingenuity.com).

source_name: Human breast cancer patient FFPE sample

label_protocol: NanoString's labeling protocol usees colo-coded probes (reporter and capture probes) to identify and detect target molecules in a sample.

extract_protocol: RNA was extracted using miRNeasy FFPE kit (Qiagen)

value: breast cancer

tag: recurrence

value: No Recurrence

tag: subtype

tag: recurrence type


title: P46L

value: Lumi A


title: E16.5, p18mKO2+, rep2


title: DNMT1-2_repeat

description:
sample name:
52681


title: OT-1 cell, sgTnfaip3-2, co-culture with cancer cell, rep1


title: OT-1 cell, sgTnfaip3-1, co-culture with cancer cell, rep3


title: P49R


title: P44R

value: Lumi B


title: Treg from Crlf2fl/fl Foxp3YFP-Cre rep1

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
Library name: Sample8
Treg from Crlf2fl/fl Foxp3YFP-Cre rep1

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Assembly: mm10/GRCm38
Supplementary files format and content: Gene expression in text format, content include gene name, symbol, chromosome, length of transcripts, and raw reads

source_name: allergic lung tissue

growth_protocol: For nTregs cultured without TCR stimulation, the sequencing libraries were constructed from 10 ng of total RNA using the Takara Bio’s SMART-Seq V4 Ultra Low Input RNA Kit for Sequencing (Cat# 634888) following the manufacturer’s instruction. For TCR-stimulated nTregs, Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero was used.

extract_protocol:
Cells were harvested and the RNA-seq libraries were prepared with 100 -500 ng of total RNA according to the manufacturer’s instructions.
The fragment size of RNA-seq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentration were determined using Qubit (LifeTech). The libraries were loaded onto the Illumina’s NovaSeq 6000 to generate 50 bp single end sequencing reads.

treatment_protocol: nTregs were stimulated with TCR (anti-CD3 + anti-CD28) in the absence versus presence of TSLP. Foxp3YFP-Cre/YCrlf2fl/fl and Foxp3YFP-Cre Tregs were isolated from allergic lung tissue

value: allergic lung tissue

tag: strain

value: Treg

value: conditional Knock-out

value: OVA-immunized


title: E13.5, p18mKO2+, rep2


title: OT-1 cell, sgTnfaip3-1, co-culture with cancer cell, rep2


title: P45R


title: control-3_repeat

description:
sample name:
52679

value: control = wildtype


title: E13.5, p18mKO2+, rep1


title: OT-1 cell, sgTnfaip3-1, co-culture with cancer cell, rep1


title: E16.5, p18mKO2-, rep3

value: normal


title: P43R


title: control-1_repeat

description:
sample name:
52677


title: E13.5, p18mKO2-, rep3

value: dorsal cortex


title: P42L


title: P41L


title: OT-1 cell, sgCtrl, co-culture with cancer cell, rep3

value: control knockout


title: OT-1 cell, sgCtrl, co-culture with cancer cell, rep2


title: DNMT1/L1TD1-3

description:
sample name:
52685


title: DNMT1/L1TD1-2

description:
sample name:
52684


title: E16.5, p18mKO2-, rep2

value: Tamoxifen administration


title: E13.5, p18mKO2-, rep2


title: E16.5, p18mKO2+, rep1

value: p18mKO2 over-expression


title: P38R


title: OT-1 cell, untreated, sgCtrl, rep3


title: DNMT1/L1TD1-1

description:
sample name:
52683

value: male

value: HAP1 cells


title: control-2_repeat

description:
sample name:
52678


title: E16.5, p18mKO2-, rep1


title: P39L


title: P40L


title: DNMT1-3

description:
sample name:
52682


title: OT-1 cell, untreated, sgCtrl, rep1

value: CD8+ T cell


title: DNMT1-2

description:
sample name:
52681


title: E13.5, p18mKO2-, rep1


title: OT-1 cell, untreated, sgCtrl, rep2


title: OT-1 cell, sgCtrl, co-culture with cancer cell, rep1


title: DNMT1-1

description:
sample name:
52680


title: BMDM, KO, H3K4me3, ChIP, rep2

city: Xiamen

first: Bin

last: Xu

address: Room 112, Chengzhi building, School of Medicine, Xiamen University, Xiang'an South Road, Xiang'an District

institute: Xiamen University

library_source: genomic

data_processing:
Raw reads were mapped to the mouse genome (mm10) using Bowtie2 (version 2.4.4).
All unmapped reads, nonuniquely mapped reads, and PCR duplicates were removed by SAMTools. Resulting SAM files were converted to BAM files by SAM tools.
We used the MACS3 version 3.0.0 peak finding algorithm to identify regions of IP enrichment over background.
The BAM files were subsequently used to generate IP/Input profiles across 5kb surrounding each gene body (TSS-TES) using deepTools (version 3.5.1).
Visualization of peak distribution along genomic regions of interested genes was performed with the Integrative Genomics Viewer (IGV).
Assembly: Mus musculus reference genome〔GRCm38 (mm10)〕
Supplementary files format and content: BigWig, generate IP/Input profiles across 5kb surrounding each gene body (TSS-TES) using deepTools (version 3.5.1)

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: BM cells isolated from the femurs and tibias were cultured in complete DMEM containing 10 ng/ml M-CSF. Isolated BMDMs were differentiated into M0 stage for 6-7 days in the presence of M-CSF.

extract_protocol:
ChIP assays were conducted with the indicated antibodies according to the instructions of the ChIP Assay kit (Millipore)
The purified DNA fragments were delivered to Novogene Biotech Co., Ltd. in dry ice according to the sample delivery instructions. DNA quantification and qualification were monitored by agarose gels, NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). Library preparation and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophage

tag: antibody


title: control-3

description:
sample name:
52679


title: f-572

city: guangzhou

first: yabing

last: xiong

address: 1838 North Guangzhou Avenue

institute: southern medical university

data_processing:
Quality control: clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each samples
Supplementary files format and content: tab-delimited text files includes FPKM for each samples

source_name: kidney

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: kidney

value: fat-1 knockin


title: BMDM, KO, H3K4me3, input, rep2

value: input


title: BMDM, KO, H3K4me3, ChIP, rep1


title: f-569


title: control-2

description:
sample name:
52678


title: P34R

value: breast cancer

value: No Recurrence

value: Lumi A


title: P33R

value: Lumi B


title: f-528


title: BMDM, KO, H3K4me3, input, rep1


title: control-1

description:
sample name:
52677

value: control = wildtype


title: PN3-male-KO

city: Philadelphia

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd

department: Dermatology

institute: University of Pennsylvania

data_processing:
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: FASTQ files, DESeq2 output

source_name: Epidermis

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA-seq NEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina

value: Epidermis

tag: gender

value: AclyKO


title: BMDM, WT, H3K4me3, ChIP, rep2

value: WT


title: P37L


title: P36R


title: KO_RNA-seq_Rep2

city: San Antonio

first: Yu

last: Luan

state: Texas

address: 7703 Floyd Curl Drive

department: Cell Systems and Anatomy

institute: University of Texas Health Science Center at San Antonio

description: RNA-seq

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM
Assembly: mm10(Mus musculus)
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: Bone Marrow HSCs

growth_protocol: Mice were raised in a standard pathogen-free animal facility and fed normal chow. Regular light/dark cycles.

extract_protocol:
Qiagen Rneasy Kit
PolyA Selection and NEBNext Ultra II Directional kit

treatment_protocol: Tissue cryopreserved in RNAlater after cell sorting

value: Bone Marrow HSCs

value: ltHSC


title: P32L

value: Local Regional Recurrence

value: Recurrence


title: BMDM, WT, H3K4me3, input, rep2

value: Bone marrow

value: BMDM


title: BMDM, WT, H3K4me3, ChIP, rep1

value: Bone marrow derived macrophage


title: P31R


title: KO_RNA-seq_Rep1

description: RNA-seq


title: 24-1

value: kidney


title: P31L


title: Control_RNA-seq_Rep2

description: RNA-seq


title: P35L


title: BMDM, WT, H3K4me3, input, rep1

value: input


title: D7, replicate 1, scRNAseq

city: shanghai

first: linxi

last: huang

address: 168 changhai road

institute: Changhai Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Freshly collected kidney cells from glyoxylate treated mice were transported in sterile culture dish with 10 ml 1X Dulbecco’s Phosphate-Buffered Saline (DPBS, Thermo Fisher, 14190144) on ice to remove the tissue storage solution, then minced on ice. Tissues were digested with 0.25% Trypsin (Thermo Fisher, 25200-072) and 10 µg/ml IDNase I (Sigma, 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS, Thermo Fisher, SV30087.02). Tissues were dissociated at 37℃ with a shaking speed of 50 rpm for about 40 minutes. Cells were repeatedly collected at interval of 20 minutes to increase cell yield and viability. Cell suspensions were filtered using 40 µm nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, 00-4333-57). Dissociated cells were washed with 1 X DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher).
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.

treatment_protocol: Male C57BL/6 mice receiving intraperitoneal injection of glyoxylate for successive 0, 1, 4 and 7 days and analyzed using scRNAseq.

tag: time point

value: renal cells

tag: age

value: 6-8 weeks old


title: BMDM, KO, H3K36me3, ChIP, rep2


title: D4, replicate 1, scRNAseq

description: 10x Genomics


title: P30L

value: breast cancer

value: No Recurrence

value: Lumi A


title: KO_ATAC-seq_Rep2

description: ATAC-seq

data_processing:
ATAC-seq reads were aligned to mm10 genome assembly using Bowtie2;ATAC-seq peak were called using MACS2 with the following  setting: ATAC-seq: q-value<10e-2 and p-value<10e-5.
Assembly: mm10(Mus musculus)
Supplementary files format and content: Tab-separated values files and matrix files ; the narrowPeak files included the peaks for each Sample

extract_protocol:
The live cells were collected, washed once in PBS and resuspended in 50 ul ATAC-seq lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) followed by immediate centrifugation for 10 min at 4 °C. Cell pellets were then resuspended in 50 ul reaction solution which contained 1XTD buffer and 2.5 ul Tn5 transpose (Illumina, FC121-1030) and incubated at 37 °C for 60 mins. The fragmented DNA was purified by the MinElute kit (Qiagen) and amplified by PCR. The final product was checked by size distribution and concentration using the BioAnalyzer High Sensitivity DNA Kit (Agilent).
Tagmentation was performed immediately according to ATAC-seq protocol reported previously(Buenrostro et al., 2013)

treatment_protocol: Tissue cryopreserved after cell sorting


title: 24-3


title: P29L


title: BMDM, KO, H3K36me3, ChIP, rep1


title: 24-2


title: KO_ATAC-seq_Rep1

description: ATAC-seq


title: D0, replicate 1, scRNAseq

description: 10x Genomics


title: D1, replicate 1, scRNAseq

description: 10x Genomics


title: P27R


title: P28L


title: BMDM, KO, H3K36me3, input, rep1


title: Control_ATAC-seq_Rep2

description: ATAC-seq


title: BMDM, WT, H3K36me3, ChIP, rep2


title: Control_ATAC-seq_Rep1

description: ATAC-seq


title: P26R

value: Lumi B


title: IgG-RIP

city: Taiepi

first: Ming-Chia

last: Lee

address: Library, Info & Research Bldg, Rm 904 #155, Sec. 2, Li-Nong St

department: Department of Life Sciences and Institute of Genome Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using topcoat (Bowtie2 [2.0.6.0] and Samtools [0.1.18.0]) at Carnegie institute for Science
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks.
Genome_build: dm6
Supplementary_files_format_and_content: abundance measurements

organism: Drosophila melanogaster

source_name: Fly ovary

growth_protocol: Oregon-R flies were raised under standard fly culture condition. For each RIP experiment,  ~200 young females (12hr post eclosion) were collected for dissecting out oavries.

extract_protocol:
Collected ovaries were transferred into RIP buffer and then homogenized, lysed, and centrifuged to acquire ovarian lysate.
Library was prepared using iIlumina TruSeq RNA Sample Prep Kit v2 (Guide Revision F). The polyA selection steps were skipped, and samples were proceed directly to Fragmentation and Priming and cDNA synthesis.

treatment_protocol: Ovarian lysate collected from young females was spited into two reactions for adding anti-GFP or anti-Lsd1 antibody respectively.

value: Ovarian lysate

tag: developmental stage

value: young females (<12 hours post eclosion)

value: Oregon-R

tag: rip antibody

value: anti-GFP (Invitrogen #A-11122)


title: P25L


title: Control_RNA-seq_Rep1

description: RNA-seq

value: Bone Marrow HSCs

value: ltHSC

value: WT


title: BMDM, WT, H3K36me3, input, rep2

value: Bone marrow

value: BMDM


title: P24L

value: Distant Recurrence

value: Recurrence


title: Lsd1-RIP

value: anti-Lsd1 (a gift from M. Buszczak)


title: BMDM, KO, H3K36me3, input, rep2

value: Bone marrow derived macrophage

value: input


title: BMDM, WT, H3K36me3, ChIP, rep1


title: DNMT1-1_repeat

description:
sample name:
52680

value: male

value: HAP1 cells


title: RS_HS_MCF7_sicircFOXK2-1

city: xiamen

first: ruichao

last: nie

state: 福建Fujian

address: xiangshanlu

institute: xiamen university

description: Library name: RS_HS_MCF7_sicircFOXK2-1

data_processing:
Low-quality reads were cleaned through Fastqc (version 0.11.9) and Fastp (version 0.22.0), two packages for sequence pre-disposal. Processed reads were aligned to human reference genome hg38 using STAR (version 2.7.11b). The alignment results were processed using the SourceForge Subread package featureCount (version 2.0.6) for gene quantification with the option -primary (count primary alignments only) -B (only count read pairs that have both ends aligned) -C (do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosomes but on different strands) -Q 20 (the minimum mapping quality score 20) -s 0 (unstranded).
Assembly: hg38
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: cell line

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L) and paired-end sequencing was performed with Illumina HiSeq 4000 platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: MCF7 cells transfected with control siRNA (siCTL) or two independent siRNAs specifically targeting circFOXK2 (si-circFOXK2-1 and si-circFOXK2-2)

value: breast cancer cells


title: RS_HS_MCF7_siCTL

description: Library name: RS_HS_MCF7_siCTL


title: RS_HS_MCF7_sicircFOXK2-2

description: Library name: RS_HS_MCF7_sicircFOXK2-2


title: BMDM, WT, H3K36me3, input, rep1


title: P23L

value: breast cancer

value: Local Regional Recurrence

value: Lumi A


title: RNA-Seq of pHNSHP45-1

city: Guangzhou

first: lin

last: jianzhong

state: Guangzhou

address: China

institute: University of Chinese Academy of Sciences

description:
Library name: pHNSHP45-1
B_1

data_processing:
After quantification with TBS380, paired-end libraries were subjected to sequencing using the Illumina NovaSeq 6000 platform (Shanghai BIOZERON Co., Ltd.). The raw paired-end reads were trimmed and quality controlled by Trimmomatic with specific parameters.
The clean reads were subsequently aligned separately to the reference K-12 and p45 genomes (GenBank accession numbers: NZ_CP009273.1 and NZ_KP347127.1) in orientation mode using Rockhopper software (51). The expression level of each transcript was calculated via the reads per kilobase per million mapped reads (RPKM) method.
Assembly: NZ_CP009273.1 and NZ_KP347127.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: vernight cultures of K-12/p45 were diluted to an initial OD600 of approximately 0.1 and then cultivated in LB for 6 h at 37 °C.

extract_protocol:
Total RNA was extracted from the cells via TRIzol® Reagent following the manufacturer’s instructions (Invitrogen), with the genomic DNA removed via the addition of 10 μL of 5 U/μL DNase I (Takara).
The RNA quality was subsequently determined using a 2100 Bioanalyzer (Agilent) and quantified using an ND-2000 (NanoDrop Technologies). High-quality RNAs (RIN>8) were utilized for the construction of sequencing libraries. The RNA-seq strand-specific libraries were prepared using a TruSeq RNA Sample Preparation Kit from Illumina (San Diego, CA) with 5 μg of total RNA. The process involved removing rRNA with the RiboZero rRNA removal kit (Epicenter), followed by fragmentation using fragmentation buffer. Further steps included cDNA synthesis, end repair, A-base addition, and ligation of Illumina-indexed adaptors, which strictly followed Illumina's protocol. Libraries were then size selected for cDNA target fragments of 200–300 bp on 2% low-range ultra agarose followed by PCR amplification via Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantification with TBS380, paired-end libraries were subjected to sequencing using the Illumina NovaSeq 6000 platform (Shanghai BIOZERON Co., Ltd.). The raw paired-end reads were trimmed and quality controlled by Trimmomatic with specific parameters

value: bacterial cell


title: RNA-Seq of pHNSHP45-3

description:
Library name: pHNSHP45-3
B_3


title: RNA-Seq of pHNSHP45-2

description:
Library name: pHNSHP45-2
B_2


title: P22L

value: Lumi B


title: GFRa1+/Kit-, cryptorchid RNA, rep03

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

country: Japan

institute: Yokohama City University

data_processing:
RNA-seq reads were quality-checked with FastQC (version 0.11.8, Babraham Bioinformatics), trimmed using Trim Galore! (version 0.6.6, Babraham Bioinformatics) and mapped with Hisat2 (version 2.1.0) on the mm10 mouse genome using default parameters. Read count (log2 RPM) was performed by using SeqMonk (version 1.48.1, Babraham Bioinformatics) for protein coding genes.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes log2-transformed rpm values for each sample.

source_name: Testis

growth_protocol: GFRa1+/Kit- spermatogonia were sorted from control testes and surgically-induced cryptorchid testes (day 10 after surgery).

extract_protocol:
RNA-seq
Nextera XT DNA Library Prep Kit

treatment_protocol: Total RNA from ~200 cells was used for RNA-seq library preparation using the Smart-seq2 protocol.

value: Testis

value: Spermatogonia

value: Cryptorchid


title: lymph node, Q2:S356-S4725-S9856, scRNA-seq BCR enriched

city: Punta Arenas

first: Julieta

last: Sepulveda Yanez

state: Magallanes Region

address: Av. Bulnes

country: Chile

institute: University of Magallanes

description:
10x Genomics
UMI_consensus_all.csv.gz
shm_all.csv.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 (scRNA-seq) and vdj_GRCh38_alts_ensembl-3.1.0 (scBCR-seq) as references
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (scRNA-seq)
Supplementary files format and content: Comma separated output files (scBCR-seq)
Supplementary files format and content: UMI_consensus_all.csv.gz; represents all the consensus by UMI for every cell barcode. The column subject indicates the subject ID and the immunoglobulin chain (HC: Heavy Chain and LC: Light Chain).
Supplementary files format and content: shm_all.csv.gz; represents neovariants found in a same gene in a particular cell. The column subject indicates the subject ID and the immunoglobulin chain (HC: Heavy Chain and LC: Light Chain).
Library strategy: scBCR-seq

source_name: lymph node

extract_protocol:
Single-cell suspensions were obtained by gentle mechanical disruption and mesh filtration and were cryopreserved using 10% DMSO as cryoprotectant. Thawed single FL cells were purified by flow cytometry using fluorescently labeled antibodies specific for CD19 and CD10 and rested overnight, followed by removal of dead cells using the MACS dead cell removal kit (Miltenyi Biotec).
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).
scRNA-seq and scRNA-seq BCR enriched

value: lymph node

value: B cell

tag: status sample

value: fresh

tag: experiment id (chip)

tag: experimental design

value: Multiple sample by chip

tag: samples


title: BMDM, KO, SETD2, input, rep2

tag: tissue

value: Bone marrow

tag: cell line

value: BMDM

value: Bone marrow derived macrophage

tag: genotype


title: lymph node, Q2:S356-S4725-S9856, scRNA-seq full transcriptome

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 (scRNA-seq) and vdj_GRCh38_alts_ensembl-3.1.0 (scBCR-seq) as references
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (scRNA-seq)
Supplementary files format and content: Comma separated output files (scBCR-seq)
Supplementary files format and content: UMI_consensus_all.csv.gz; represents all the consensus by UMI for every cell barcode. The column subject indicates the subject ID and the immunoglobulin chain (HC: Heavy Chain and LC: Light Chain).
Supplementary files format and content: shm_all.csv.gz; represents neovariants found in a same gene in a particular cell. The column subject indicates the subject ID and the immunoglobulin chain (HC: Heavy Chain and LC: Light Chain).

tag: cell type


title: GFRa1+/Kit-, cryptorchid RNA, rep02


title: P20R

tag: recurrence

value: Distant Recurrence

tag: subtype

value: Recurrence


title: P21L

value: breast cancer

value: No Recurrence

tag: recurrence type


title: GFRa1+/Kit-, cryptorchid RNA, rep01


title: lymph node, Q1:S5714-S7482, scRNA-seq BCR enriched


title: BMDM, KO, SETD2, ChIP, rep1

tag: antibody


title: GFRa1+/Kit-, control RNA, rep03

value: WT


title: lymph node, Q1:S5714-S7482, scRNA-seq full transcriptome

description: 10x Genomics


title: P19L

value: Lumi A


title: BMDM, KO, SETD2, input, rep1

value: input


title: P18L


title: GFRa1+/Kit-, control RNA, rep02

value: Testis


title: lymph node, K8B:S13553, scRNA-seq full transcriptome

description: 10x Genomics

value: Unique sample by chip


title: BMDM, WT, SETD2, ChIP, rep2


title: P17L


title: GFRa1+/Kit-, control RNA, rep01

value: Spermatogonia


title: lymph node, K7B:S10000, scRNA-seq BCR enriched

value: lymph node


title: BMDM, WT, SETD2, ChIP, rep1


title: GFRa1+/Kit-, cryptorchid H3K9me3, rep01

data_processing:
ChIP-seq reads were quality-checked (FastQC; Babraham Bioinformatics), adapter- and quality-trimmed (Trim Galore! version 0.6.6; Babraham Bioinformatics), and mapped onto the mouse genome (mm10) using Bowtie 2 version 2.5.1 with the parameter -N 1. After quality filtering, duplicates were removed with Picard. ChIP-seq peak identification and read count were performed using SeqMonk/MACS2 (version 1.48.1, Babraham Bioinformatics) with the default parameter.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
ChIP-seq
ChIP-seq libraries were constructed with the CATCH-seq method (Nat Cell Biol, doi: 10.1038/s41556-024-01553-1).

treatment_protocol: About 1,000 to 2,000 cells were used for H3K27me3 and H3K9me3 ChIP-seq experiments.

value: Cryptorchid

tag: treatment


title: BMDM, KO, SETD2, ChIP, rep2


title: P15R


title: P16R


title: lymph node, K6B:S13530, scRNA-seq BCR enriched

value: B cell

value: fresh


title: BMDM, WT, SETD2, input, rep1

value: Bone marrow


title: GFRa1+/Kit-, cryptorchid H3K27me3, rep02


title: GFRa1+/Kit-, cryptorchid H3K27me3, rep01


title: P14R


title: P13R


title: lymph node, K7B:S10000, scRNA-seq full transcriptome

description: 10x Genomics


title: BMDM, WT, menin, ChIP, rep2

value: BMDM

value: menin


title: GFRa1+/Kit-, control H3K9me3, rep01


title: GFRa1+/Kit-, control H3K27me3, rep02


title: lymph node, K8B:S13553, scRNA-seq BCR enriched


title: lymph node, K6B:S13530, scRNA-seq full transcriptome

description: 10x Genomics


title: BMDM, WT, menin, input, rep2

value: Bone marrow derived macrophage


title: BMDM, WT, menin, ChIP, rep1


title: P12L


title: P11L

value: Distant Recurrence

value: Lumi B

value: Recurrence


title: BMDM, WT, menin, input, rep1

value: WT


title: GFRa1+/Kit-, control H3K27me3, rep01


title: lymph node, K4B:S8934, scRNA-seq BCR enriched


title: BMDM, WT, SETD2, input, rep2


title: lymph node, K5B:S8934, scRNA-seq full transcriptome

description: 10x Genomics


title: P10L

value: breast cancer


title: lymph node, K4B:S8934, scRNA-seq full transcriptome

description: 10x Genomics


title: P09R

value: Lumi A


title: ADSC_Aligned

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

institute: Zhejiang University

data_processing:
The sequencing data were processed with default parameters using DLO Hi-C tool as previously described:"Hong, P. et al. The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis. Genes (Basel)  11(3):289 (2020) "
Assembly: mm10
Supplementary files format and content: hic contact matrix in cool format

source_name: Adipose

growth_protocol: MSCs were isolated from the abdominal subcutaneous fat of C57BL/6 mice. The adipose tissues were cut up and digested for about 2 hours at 37°C using collagenase type I. Then the cell suspension solutions were centrifuged at 1500 rpm for 10 min and resuspended in Dulbecco’s Modified Eagle Medium (DMEM) containing 1 g/L of glucose (Gibco) with 10% FBS (Gibco) and 1% penicillin/streptomycin (Life Technologies) to generate primary mice MSCs cultures.

extract_protocol:
About 1 million cells were pelleted and cross-linked with 1% methanol-free formaldehyde for 10min at room temperature, and quenched with 125 mM glycine. Then the cells were treated with lysis buffer and cell nuclei were pelleted by centrifuging. The nuclei were then incubated with restriction enzyme MseI. After enzyme digestion, a biotin-linker was added to the chromatin fragment, followed by fragment-end phosphorylation and in situ proximity ligation. After ligation, reversal of cross-linking was performed by adding proteinase K and 10% SDS to the reaction product, and DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1).
In situ DLO Hi-C libraries were constructed as previously described: “Lin, D. et al. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature genetics 50, 754 (2018).”

treatment_protocol: Cells were cultured on the petri dish, aligned scaffold and random scaffold for 3 days.

value: Adipose

tag: strain

value: Adipose derived mesenchymal stem cells

value: Wild type

value: Cells were cultured on aligned scaffold


title: ADSC_Random

value: Cells were cultured on random scaffold


title: F_WT_5638

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: GRCm38 (mm10)
Supplementary files format and content: count and FPKM values for each sample
Supplementary files format and content: differential analysis of all genes and all the differential genes  between M-WT and M-KO samples

source_name: peritoneal cavity

extract_protocol:
Peritoneal cavity macrophage was isolated and sent to Novogene Co., Ltd. Beijing, China.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: peritoneal cavity

value: macrophage

value: thioglycollate broth stimulation


title: ADSC_Control

value: Control


title: lymph node, K3B:S12390-S12500-S8382-S8934, scRNA-seq BCR enriched

value: lymph node

value: B cell

value: fresh

value: Multiple sample by chip


title: P07L

data_processing: All NanoString gene expression data analysis was performed using nSolver Analysis Software v3.0 (NanoString Technologies, Seattle, WA). Raw data was normalized by subtracting the mean plus one standard deviation of eight negative controls while technical variation was normalized through internal positive controls. Data was corrected for input volume via eight internal housekeeping genes using the geNorm algorithm. Clinical, tumor, and patient characteristics were analyzed in relation to recurrence status. Relative gene expression was analyzed by recurrence status. PAM50 subtype analysis was performed to identify molecular subtypes. Bioinformatics analysis was performed based on the ingenuity pathway analysis (IPA) tool (version 73620684, http://www.ingenuity.com).

value: Local Regional Recurrence

value: Lumi B

value: Recurrence


title: P08L

value: breast cancer


title: lymph node, K3B:S12390-S12500-S8382-S8934, scRNA-seq full transcriptome

description: 10x Genomics


title: lymph node, K5B:S8934, scRNA-seq BCR enriched

value: Unique sample by chip


title: ADSC_Random_ATAC

data_processing:
ATAC-seq sequencing reads were aligned to mm10 using Bowtie2 with parameters -X 2000. Duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/). Read with mapping quality < 30 were removed with Samtools. All reads aligned to the positive strands were offset by +4 bp and all reads aligned to the negative strands were offset by −5 bp. ATAC-seq peaks were defined using the MACS2 callpeaks function. Bigwig tracks were generated using deepTools by normalizing to RPKM using binsize of 10 bp. ATAC-seq signal over region of interest were visualized using deepTools. Motif annotation over ATAC peak summits was performed using Homer findMotifsGenome.pl function.
Assembly: mm10
Supplementary files format and content: Normalized and replicate-combined bigWig files, reporting the ATAC signals

extract_protocol:
Nuclei were isolated before transposition. Briefly, approximately 50,000 cells were collected and rinsed with cold PBS. The cells were then suspended in 50 ul lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) and  incubated on ice for 10min. The nuclei were then collected by centrifugation at 500 g for 5 minutes at 4℃.ŸRŹ_x0006_ƣR_x0001__x000C_=7_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000_ʯ_x0000_ÿATAC-seq sequencing reads were aligned to m
ATAC-seq libraries was prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501) according to manufacturer’s instructions

value: Adipose

value: Adipose derived mesenchymal stem cells


title: M_KO_5645

value: KO


title: lymph node, K2B:S11770-S12118-S12500-S13530-S13553, scRNA-seq BCR enriched


title: P06L

extract_protocol: RNA was extracted using miRNeasy FFPE kit (Qiagen)

value: Lumi A


title: P05R

value: No Recurrence


title: F_KO_5639

value: peritoneal cavity

value: macrophage


title: lymph node, K1B:S10000-S10971-S12282-S144-S8934, scRNA-seq BCR enriched


title: lymph node, K2B:S11770-S12118-S12500-S13530-S13553 , scRNA-seq full transcriptome

description: 10x Genomics


title: ADSC_Aligned_ATAC

value: Wild type

value: Cells were cultured on aligned scaffold


title: M_WT_6255

value: WT

value: thioglycollate broth stimulation


title: ADSC_Control_ATAC

value: Control


title: M_WT_6258


title: P04L


title: d15

city: Osaka

first: Yu-Tung

address: 2-2 Yamada-oka, Suita

institute: Osaka University

data_processing:
Fastq files were aligned to Mus musculus mm10 reference with Cell Ranger (v4.0.0) using function cellranger count.
Files from different samples were then aggregated by Cell Ranger (v4.0.0) to construct count tables (genes as rows and cells as columns) with function cellranger aggr.
Assembly: mm10
Supplementary files format and content: Processed data files are zipped aggregated output directory of Cell Ranger.

source_name: Mouse skin cells

growth_protocol: (cells were isolated directly from tissues without culture)

extract_protocol:
On day 0 (unstimulated), 8 and 15 post-induction (equivalent to 0, 4 and 7 doses), skin samples (3-4 mice pooled per sample) were excised and digested in 0.3% collagenase-A, 0.25mg/ml Dispase-II, 10U/ml DNaseI and 2%FBS in RPMI for one hour to obtain single cell suspension. FcR was blocked with 2.4G2 before incubating with anti-CD45-magnetic beads (Biolegend, #480028). Magnetically isolated cells were subjected to sequencing profiling.
Library was prepared with Chromium Single Cell 3’ Reagent Kits (v3.1 Chemistry; 10x Genomics). The 3’ gene expression libraries with paired-end Read 1 (containing 16-bp barcode and 12-bp UMI), Read 2 (91-bp insert) and i7 index (8-bp) were analysed by Illumina HiSeq X.

treatment_protocol: Dorsal skin received topically dose of 10nmol MC903 bi- or tri-daily.

value: Skin

value: CD45+ bead enriched


title: M_KO_5642


title: d8


title: VSV, scRNAseq

city: Shanghai

first: Shulei

last: Yin

state: Shanghai

address: No.800 Xiangyin Road, Yangpu District

department: Department of Immunology

institute: Naval Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Single cell matrix files

source_name: lung

extract_protocol:
Pulmonary artery tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: lung

value: lung cells


title: M_WT_5643


title: P03R

value: breast cancer


title: P02R

value: Lumi B


title: H1-derived patterned endoderm scRNA-seq

city: Stanford

first: Lay Teng

last: Ang

address: Institute for Stem Cell Biology & Regenerative Medicine, Lokey Stem Cell Bldg, 265 Campus Drive

department: Urology

institute: Stanford University

description:
Library name: H1-Gut
10x genomics library

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software 6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human embryonic stem cell

extract_protocol:
scRNAseq was performed on cells recovered from six separate cell culture channels after day 5 of differentiation. First, reservoirs at either side of the channel were drained using a pipette. Accutase was added at 37 oC for 5 min to dissociate cells from the microfluidic chip. The device was examined under the microscope to check for cell detachment from the central channel before Accutase was quenched in DMEM/F12. The following steps were adapted from the 10X Genomics Single Cell Protocols. After dissociation, the cell suspension was strained through a single cell strainer and centrifuged at 500 rcf for 5 min. Dead cells were filtered out using the Miltenyi MACS Dead Cell Removal Kit (Miltenyi Biotech, Gaithersburg, MD), and the live cells were centrifuged again at 500 rcf for 5 min. The binding buffer that remained from the dead cell removal process was gently removed, and the remaining cells were resuspended in DMEM/F12. An automated cell counter (TC20, Bio-Rad, Hercules, California) was used to count the cells, which were later centrifuged at 500 rcf for 5 min. The supernatant was gently aspirated with a pipette and replaced with DMEM/F12 containing 10% Fetal Bovine Serum to reach a total volume of 50 µL. Cells were sent to the Stanford Genomics Core for sequencing and a library was prepared using the 10x Chromium Single Cell 3’ v3.1 NextGEM system. Data was further analyzed using Seurat v3.
Library was performed according to manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: Directed differentiation of H1 human embryonic stem cells in a dish

value: Human embryonic stem cell

value: Anterior and posterior endoderm

tag: Sex

value: Male

value: Differentiation in vitro

tag: time

value: day 5


title: P01L

value: No Recurrence

value: Lumi A


title: M_KO_5944

value: peritoneal cavity

value: macrophage

value: KO


title: SRR16473454_se_0_ys_pe

status: Public on Dec 24 2024

city: Beijing

first: Yi

last: Zheng

address: No. 7, Beinong Road, Huilongguan Town, Changping District

institute: Beijing University of Agriculture

description: Library name: Sample 10

data_processing:
RNA-Seq reads were processed with FastQC (v0.11.9), trimmed with Trimmomatic, aligned using STAR (v2.7.10b), and normalized to FPKM values.
Assembly: GCA_014183005.1
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Castanea mollissima

source_name: somatic embryo 10

extract_protocol:
Plant Total RNA Extraction Kit
Directional RNA Library Prep Kit for Illumina following the manufacturer’s protocols.

value: somatic embryo 10


title: SRR16473448_c_0_ys_pe

description: Library name: Sample 15

source_name: callus 3

value: callus 3


title: SRR16473451_c_0_ys_pe

description: Library name: Sample 18

source_name: callus 6

value: callus 6


title: SRR16473442_c_0_ys_pe

description: Library name: Sample 13

source_name: callus 1

value: callus 1


title: SRR16473455_se_0_ys_pe

description: Library name: Sample 11

source_name: somatic embryo 11

value: somatic embryo 11


title: SRR16473449_c_0_ys_pe

description: Library name: Sample 16

source_name: callus 4

value: callus 4


title: SRR16473453_se_0_ys_pe

description: Library name: Sample 9

source_name: somatic embryo 9

value: somatic embryo 9


title: SRR16473447_se_0_ys_pe

description: Library name: Sample 7

source_name: somatic embryo 7

value: somatic embryo 7


title: SRR16473443_c_0_ys_pe

description: Library name: Sample 14

source_name: callus 2

value: callus 2


title: SRR16473446_se_0_ys_pe

description: Library name: Sample 6

source_name: somatic embryo 6

value: somatic embryo 6


title: SRR16473450_c_0_ys_pe

description: Library name: Sample 17

source_name: callus 5

value: callus 5


title: SRR16473452_se_0_ys_pe

description: Library name: Sample 8

source_name: somatic embryo 8

value: somatic embryo 8


title: SRR16473445_se_0_ys_pe

description: Library name: Sample 5

source_name: somatic embryo 5

value: somatic embryo 5


title: SRR16473444_se_0_ys_pe

description: Library name: Sample 4

source_name: somatic embryo 4

value: somatic embryo 4


title: lymph node, K1B:S10000-S10971-S12282-S144-S8934, scRNA-seq full transcriptome

description: 10x Genomics

source_name: lymph node

value: lymph node

value: B cell

value: fresh

value: Multiple sample by chip


title: SRR16473439_se_0_ys_pe

description: Library name: Sample 1

source_name: somatic embryo 1

value: somatic embryo 1


title: d0

source_name: Mouse skin cells

value: Skin

value: CD45+ bead enriched


title: SRR16473440_se_0_ys_pe

description: Library name: Sample 2

source_name: somatic embryo 2

value: somatic embryo 2


title: U2OS cells, BMH-21, UBF (ChIP), rep2

city: Eugene

first: Victoria

last: DeRose

state: Oregon

address: 1370 Franklin Blvd.

department: Chemistry and Biochemistry

institute: University of Oregon

description: Library name: U2OS_BMH21_UBF_ChIP-rep2

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.39, discarding reads with a quality score < 15 or under 30 bp in length.
ChIP-seq reads were aligned to custom human genome assemble generated from T2T-CHM13 genome using Bowtie2 v2.5.4 permitting for mulitple alignments and indel variations up to 2 kb.
Sequence alignment maps were filtered using Samtools v1.19 to remove unmapped reads while retaining multimapped reads.
ChIP-seq coverage plots were generated using the deeptools package v3.5.3. Mapped ChIP-seq reads were extended to the length of the paired-end fragment, centered and smoothed using a 15 bp sliding-window, and then normalized to total counts per million reads (CPM) and reformated as bigWig files.
Assembly: Custom T2T-CHM13 genome containing a single full-length (44838 nt) human rDNA repeat (GenBank: KY962518.1) inserted as an additional chromosome (chrR).
Supplementary files format and content: bigWig, CPM counts for each sample

source_name: Bone

growth_protocol: Cells cultured at 37°C, 5% CO2, in DMEM for A549 cells or McCoy's 5A for U2OS cells, supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic.

extract_protocol:
Cells were fixed with 1% paraformaldehyde in phosphate buffered saline for 10 min at RT, then quenched with 125mM glycine. Fixed cells were lysed in RIPA buffer on ice, and chromatin was sheared using a Diagenode Bioruptor sonicator.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit, for Illumina (New England Biolabs, #E7600S) and NEBNext Ultra II DNA Library Prep Kit, for Illumina (New England Biolabs, #E7645S). 10 ng of DNA was used for input samples and for 1 ng of DNA was used IP sample. Libraries were amplified using 12 cycles on a thermocycler. Post amplification libraries were size selected at 200-400 bp in length using Omega Mag-Bind TotalPure NGS beads. Libraries were validated on an fragment analyzer using an Agilent NGS Fragment kit.

treatment_protocol: A549 or U2OS cells were treated with 10 µM cisplatin, 10 µM oxaliplatin, or 1 µM BMH-21 in cell media for 3 h at 37°C and 5% CO2.

value: Bone

value: osteosarcoma cells

tag: chip antibody

value: UBF (F-9) (Santa Cruz, sc-13125)


title: U2OS cells, cisplatin, mock IgG (ChIP), rep2

description: Library name: U2OS_CPPt_IgG_ChIP-rep2

value: Mouse IgG isotype (Invitrogen, #31903)

value: Cisplatin, 3 h


title: U2OS cells, BMH-21, Pol I (ChIP), rep2

description: Library name: U2OS_BMH21_RPA194_ChIP-rep2


title: U2OS cells, BMH-21, mock IgG (ChIP), rep2

description: Library name: U2OS_BMH21_IgG_ChIP-rep2


title: SRR16473456_se_0_ys_pe

description: Library name: Sample 12

source_name: somatic embryo 12

value: somatic embryo 12


title: U2OS cells, cisplatin, UBF (ChIP), rep2

description: Library name: U2OS_CPPt_UBF_ChIP-rep2


title: U2OS cells, BMH-21, (Input), rep2

description: Library name: U2OS_BMH21_Input-rep2


title: U2OS cells, cisplatin, Pol I (ChIP), rep2

description: Library name: U2OS_CPPt_RPA194_ChIP-rep2


title: U2OS cells, cisplatin, (Input), rep2

description: Library name: U2OS_CPPt_Input-rep2


title: U2OS cells, oxaliplatin, mock IgG (ChIP), rep2

description: Library name: U2OS_OxPt_IgG_ChIP-rep2

value: Oxaliplatin, 3 h


title: U2OS cells, oxaliplatin, UBF (ChIP), rep2

description: Library name: U2OS_OxPt_UBF_ChIP-rep2


title: U2OS cells, oxaliplatin, Pol I (ChIP), rep2

description: Library name: U2OS_OxPt_RPA194_ChIP-rep2


title: U2OS cells, control, mock IgG (ChIP), rep2

description: Library name: U2OS_Ctrl_IgG_ChIP-rep2

value: Untreated


title: U2OS cells, oxaliplatin, (Input), rep2

description: Library name: U2OS_OxPt_Input-rep2


title: U2OS cells, control, Pol I (ChIP), rep2

description: Library name: U2OS_Ctrl_RPA194_ChIP-rep2


title: U2OS cells, control, UBF (ChIP), rep2

description: Library name: U2OS_Ctrl_UBF_ChIP-rep2


title: U2OS cells, control, (Input), rep2

description: Library name: U2OS_Ctrl_Input-rep2


title: SRR16473441_se_0_ys_pe

description: Library name: Sample 3

source_name: somatic embryo 3

value: somatic embryo 3


title: Wild-Type, kidney RNAseq3

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

institute: keio university

description: Library name: control-5

data_processing: DEGs, heatmaps, and PCAs were analyzed using the DESeq2 package version 1.28.13. The enrichment of GO biological processes and the correlation network of enriched GO terms were analyzed with the clusterProfiler package, version 3.16.14, with p values of 0.01 and 0.05 and q-values of 0.05 (BH methods).

source_name: kidney cortex

extract_protocol:
Total RNA was used to prepare an RNA-seq library using the TruSeq Stranded mRNA LT Sample Prep Kit according to the TruSeq Stranded mRNA Sample Preparation Guide, part #15031047 Rev. E (Illumina, San Diego, CA, USA).
The libraries were sequenced for 100 cycles (paired ends) using a NovaSeq 6000 instrument (Illumina). The sequence reads from each RNA-seq library were mapped onto the mouse genome (mm9) using HISAT2 version 2.2.11, and the number of sequence reads for each gene was calculated using featureCounts version 1.5.2 of the Subread package2.

value: kidney cortex


title: PT-I_Ppo-1, kidney RNAseq3

description: Library name: IpPoI-Tg-4


title: Wild-Type, kidney RNAseq2

description: Library name: control-4


title: Wild-Type, kidney RNAseq1

description: Library name: control1


title: U2OS cells, BMH-21, UBF (ChIP), rep1

description: Library name: U2OS_BMH21_UBF_ChIP-rep1


title: PT-I_Ppo-1, kidney RNAseq2

description: Library name: IpPoI-Tg2


title: U2OS cells, BMH-21, Pol I (ChIP), rep1

description: Library name: U2OS_BMH21_RPA194_ChIP-rep1


title: U2OS cells, BMH-21, (Input), rep1

description: Library name: U2OS_BMH21_Input-rep1


title: hADSCs-4

first: Zijun

state: Guangdong

address: 58 Zhongshan Road II

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Gene expression of hADSCs-4

hyb_protocol: The labeled cRNAs were hybridized onto the microarray based on the manufacturer's standard protocols.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies) based on the manufacturer's standard protocols.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label_protocol: Total RNA was transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP based on the manufacturer's standard protocols.

growth_protocol: The hADSCs were cultured in 10%FBS+F12/DMEM+1%PS.

extract_protocol: RNA was harvested using Trizol reagent. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: After hADSCs reached confluence and were mantained for 48 hours, cells were then maintained in DMEM/Ham’s F12 media supplemented with 10 µg/ml of transferrin, 0.85 µM insulin, 0.2 nM triiodothyronine, 1 µM dexamethasone (DEX), and 500 µM isobutyl methylxanthine (IBMX) (designated as day 0). Three days later, the medium was changed (DEX and isobutyl methylxanthine were omitted) and 100 nM rosiglitazone were added. Media were then changed every other day until day 16.

value: human adipose derived stem cells (hADSCs)

tag: processing time

value: untreated


title: U2OS cells, cisplatin, mock IgG (ChIP), rep1

description: Library name: U2OS_CPPt_IgG_ChIP-rep1


title: I-PpoI blood, RRBS

description: Library name: Blood_Tg2

data_processing: Differential methylation was calculated using the calculateDiffMeth function of methylKit. Cytosines/Regions with a q-value below 0.01 and a methylation change larger than 25% between the groups were considered as significantly differentially methylated cytosines/regions (DMCs/DMRs).

source_name: peripheral blood cells

extract_protocol:
DNA was extracted and adjusted to a concentration of ≥30 ng/µL, OD 260/280 ≥1.8 and OD260/230 ≥1.0.
Methylation analysis of CpG regions, library preparation was performed according to the Zymo Research Zymo-Seq RRBS Library Kit (Cat No. D5460/5461) manual (Ver. 1.0.0), i.e., enrichment of CpG-rich regions by fragmentation of genomic DNA using the restriction enzyme Mspl, addition of the TruSeq adaptor, bisulfite treatment and addition of index sequences. The enriched DNA samples were amplified, and next-generation sequencing was performed.

value: peripheral blood cells


title: WT blood, RRBS

description: Library name: Blood_WT2


title: U2OS cells, cisplatin, Pol I (ChIP), rep1

description: Library name: U2OS_CPPt_RPA194_ChIP-rep1


title: U2OS cells, cisplatin, (Input), rep1

description: Library name: U2OS_CPPt_Input-rep1


title: Brown Adipocytes-1

description: Gene expression of Brown Aipocytes-1

source_name: Brown Adipocytes-1, browning of hADSCs-1, 16 days

value: brown adipocyte

value: Brown Adipocytes induction


title: U2OS cells, BMH-21, mock IgG (ChIP), rep1

description: Library name: U2OS_BMH21_IgG_ChIP-rep1


title: Brown Adipocytes-2

description: Gene expression of Brown Aipocytes-2

source_name: Brown Adipocytes-2, browning of hADSCs-2, 16 days


title: MSCs, FMT-Exer2

first: Congcong

last: Yu

address: Qingchundong road

institute: Zhejiang university

description:
Library name: Sample 5
C2

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using the RNAsimple Total RNA Kit (TIANGEN, DP419) according to the manufacturer's instructions.
The RNA-seq transcriptome library was prepared using the Illumina® Stranded mRNA Prep, Ligation from Illumina using 1 μg of total RNA.

value: Bone marrow

value: MSCs

value: OVX mice receiving fecal microbiota transplantation from exercised mice


title: MSCs, FMT-Ctrl2

description:
Library name: Sample 2
B2

value: OVX mice receiving fecal microbiota transplantation from sedentary mice


title: Brown Adipocytes-5

last: Xu

description: Gene expression of Brown Aipocytes-5

source_name: Brown Adipocytes-5, browning of hADSCs-5, 16 days


title: MSCs, FMT-Exer1

description:
Library name: Sample 4
C1


title: MSCs, FMT-Ctrl3

description:
Library name: Sample 3
B3


title: U2OS cells, oxaliplatin, UBF (ChIP), rep1

description: Library name: U2OS_OxPt_UBF_ChIP-rep1

value: Bone

value: osteosarcoma cells

value: UBF (F-9) (Santa Cruz, sc-13125)


title: PT-I_Ppo-1, kidney RNAseq1

description: Library name: IpPoI-Tg1


title: MSCs, FMT-Ctrl1

description:
Library name: Sample 1
B1


title: hADSCs-5

description: Gene expression of hADSCs-5


title: U2OS cells, oxaliplatin, (Input), rep1

description: Library name: U2OS_OxPt_Input-rep1


title: U2OS cells, cisplatin, UBF (ChIP), rep1

description: Library name: U2OS_CPPt_UBF_ChIP-rep1

value: Cisplatin, 3 h


title: Liver, Ctrl, 150day,rep2

first: Mingming

last: ZHANG

address: Taiping Road No.27

institute: AMMU

description: 10X Genomics

data_processing:
Raw and filtered feature-barcode matrices for each sample was generated using 10× Genomics Cell Ranger software v6.0.2. To filter low quality cells and enrich for high quality cells in each dataset, Quality control and doublets removal were performed for each dataset individually.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files.

source_name: Liver

extract_protocol:
Freshly collected livers from C57/BL6J mice were flushed with ice-cold PBS to remove luminal content. Dissociated for single cell RNA sequencing was performed with the Liver Dissociation kit(130-105-807, Miltenyi Biotec) according to manufacturer’s protocol. Briefly, the tissue was cut into small pieces of 2-4mm and flushed with the RPMI/enzyme mix (Miltenyi Biotec). After the gentleMACS Octo Dissociator program, the suspension was passed through a 70um straine and spun down at 300 x g for 10 min at 4 °C. Then the supernatant was added with 10 times volume 1 x Red Blood CellLysis Solution(130-094-183, Miltenyi Biotec) to lytic red blood cells in the refrigerator at 4 °C for 10 min.
Library construction was performed with Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions. Briefly, Chromium Single cell 3’ Library and Gel Bead Kit V3.1 (10× Genomics, PN1000268) was used to generate single cell gel beads in emulsion (GEM). The captured cells were lysed, and the released RNA was reverse-transcribed with primers containing poly-T, barcode, unique molecular identifiers (UMIs) and read 1 primer sequence in GEMs. Barcoded cDNA was purified and amplified by PCR. The adapter ligation reaction was performed to add sample index and read 2 primer sequence.

value: Liver

value: Male


title: MSCs, FMT-Exer3

description:
Library name: Sample 6
C3


title: U2OS cells, oxaliplatin, mock IgG (ChIP), rep1

description: Library name: U2OS_OxPt_IgG_ChIP-rep1

value: Mouse IgG isotype (Invitrogen, #31903)

value: Oxaliplatin, 3 h


title: U2OS cells, oxaliplatin, Pol I (ChIP), rep1

description: Library name: U2OS_OxPt_RPA194_ChIP-rep1


title: hADSCs-2

description: Gene expression of hADSCs-2

value: human adipose derived stem cells (hADSCs)


title: Brown Adipocytes-4

description: Gene expression of Brown Aipocytes-4

source_name: Brown Adipocytes-4, browning of hADSCs-4, 16 days


title: hADSCs-3

description: Gene expression of hADSCs-3

value: untreated


title: U2OS cells, control, mock IgG (ChIP), rep1

description: Library name: U2OS_Ctrl_IgG_ChIP-rep1

value: Untreated


title: U2OS cells, control, UBF (ChIP), rep1

description: Library name: U2OS_Ctrl_UBF_ChIP-rep1


title: hADSCs-1

description: Gene expression of hADSCs-1


title: U2OS cells, control, Pol I (ChIP), rep1

description: Library name: U2OS_Ctrl_RPA194_ChIP-rep1


title: Brown Adipocytes-3

description: Gene expression of Brown Aipocytes-3

source_name: Brown Adipocytes-3, browning of hADSCs-3, 16 days

value: brown adipocyte


title: A549 cells, BMH-21, mock IgG (ChIP), rep2

description: Library name: A549_BMH21_IgG_ChIP-rep2

source_name: Lung

value: Lung

value: epithelial cells


title: U2OS cells, control, (Input), rep1

description: Library name: U2OS_Ctrl_Input-rep1


title: Liver, EMF, 150day,rep1

description: 10X Genomics

value: 2.45 GHz electromagnetic field, 6min/day


title: A549 cells, BMH-21, Pol I (ChIP), rep2

description: Library name: A549_BMH21_RPA194_ChIP-rep2


title: Liver, Ctrl, 90day,rep1

description: 10X Genomics


title: A549 cells, BMH-21, UBF (ChIP), rep2

description: Library name: A549_BMH21_UBF_ChIP-rep2


title: KPC_SMAD4_KO_SITTD11_SLX_21289

city: Cambridge

first: Giulia

last: Biffi

address: Robinson way

country: United Kingdom

institute: University of Cambridge

data_processing:
CellRanger count (v7.0.1) : default parameters
Assembly: GRCm39 (mm39)
Supplementary files format and content: raw_feature_bc_matrix

source_name: KPC organiods

extract_protocol:
we submitted 16K cells in 43 uL
Chromium Next GEM Single Cell 3' Kit v3.1, PN-1000268; Chromium Next GEM Chip G Single Cell Kit, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide

value: PDAC tumors

value: KPC organiods

value: SMAD4 KO


title: Liver, EMF, 90day,rep1

description: 10X Genomics


title: KPC_SMAD4_KO_SITTC11_SLX_21289


title: A549 cells, BMH-21, (Input), rep2

description: Library name: A549_BMH21_Input-rep2


title: A549 cells, cisplatin, Pol I (ChIP), rep2

description: Library name: A549_CPPt_RPA194_ChIP-rep2


title: A549 cells, cisplatin, UBF (ChIP), rep2

description: Library name: A549_CPPt_UBF_ChIP-rep2


title: A549 cells, cisplatin, mock IgG (ChIP), rep2

description: Library name: A549_CPPt_IgG_ChIP-rep2


title: Liver, Ctrl, 150day,rep1

description: 10X Genomics


title: Liver, EMF, 150day,rep2

description: 10X Genomics


title: KPC_SMAD4_WT_SITTE11_SLX_21289

value: SMAD4 WT


title: A549 cells, oxaliplatin, mock IgG (ChIP), rep2

description: Library name: A549_OxPt_IgG_ChIP-rep2


title: KPC_SMAD4_KO_SITTG11_SLX_21289


title: KPC_SMAD4_KO_SITTB11_SLX_21289


title: A549 cells, oxaliplatin, UBF (ChIP), rep2

description: Library name: A549_OxPt_UBF_ChIP-rep2

value: UBF (F-9) (Santa Cruz, sc-13125)


title: A549 cells, cisplatin, (Input), rep2

description: Library name: A549_CPPt_Input-rep2

value: Cisplatin, 3 h


title: KPC_SMAD4_KO_SITTB6_SLX_21289


title: A549 cells, oxaliplatin, Pol I (ChIP), rep2

description: Library name: A549_OxPt_RPA194_ChIP-rep2


title: KPC_SMAD4_WT_SITTF11_SLX_21289


title: A549 cells, oxaliplatin, (Input), rep2

description: Library name: A549_OxPt_Input-rep2


title: KPC_SMAD4_KO_SITTG11_SLX_21116


title: A549 cells, control, mock IgG (ChIP), rep2

description: Library name: A549_Ctrl_IgG_ChIP-rep2


title: KPC_SMAD4_KO_SITTA6_SLX_21289


title: A549 cells, control, UBF (ChIP), rep2

description: Library name: A549_Ctrl_UBF_ChIP-rep2


title: KPC_SMAD4_KO_SITTD11_SLX_21116


title: KPC_SMAD4_KO_SITTB6_SLX_21116


title: A549 cells, control, (Input), rep2

description: Library name: A549_Ctrl_Input-rep2


title: A549 cells, BMH-21, mock IgG (ChIP), rep1

description: Library name: A549_BMH21_IgG_ChIP-rep1


title: KPC_SMAD4_KO_SITTA6_SLX_21116


title: KPC_SMAD4_WT_SITTF11_SLX_21116


title: A549 cells, BMH-21, UBF (ChIP), rep1

description: Library name: A549_BMH21_UBF_ChIP-rep1


title: A549 cells, control, Pol I (ChIP), rep2

description: Library name: A549_Ctrl_RPA194_ChIP-rep2


title: KPC_SMAD4_KO_SITTC11_SLX_21116


title: A549 cells, BMH-21, Pol I (ChIP), rep1

description: Library name: A549_BMH21_RPA194_ChIP-rep1


title: KPC_SMAD4_WT_SITTA11_SLX_21116


title: A549 cells, BMH-21, (Input), rep1

description: Library name: A549_BMH21_Input-rep1


title: KPC_SMAD4_KO_SITTB11_SLX_21116


title: KPC_SMAD4_WT_SITTE11_SLX_21116


title: KvPC_SMAD4_WT_SITTG4

source_name: KvPC organoids

value: KvPC organoids


title: KvPC_SMAD4_WT_SITTH4


title: KvPC_SMAD4_KO_SITTH12


title: KPC_SMAD4_WT_SITTA11_SLX_21289


title: A549 cells, cisplatin, Pol I (ChIP), rep1

description: Library name: A549_CPPt_RPA194_ChIP-rep1


title: A549 cells, oxaliplatin, mock IgG (ChIP), rep1

description: Library name: A549_OxPt_IgG_ChIP-rep1


title: KvPC_SMAD4_WT_SITTE4


title: KvPC_SMAD4_KO_SITTG12


title: A549 cells, cisplatin, (Input), rep1

description: Library name: A549_CPPt_Input-rep1


title: A549 cells, cisplatin, UBF (ChIP), rep1

description: Library name: A549_CPPt_UBF_ChIP-rep1


title: A549 cells, cisplatin, mock IgG (ChIP), rep1

description: Library name: A549_CPPt_IgG_ChIP-rep1


title: KvPC_SMAD4_WT_SITTD4


title: A549 cells, oxaliplatin, UBF (ChIP), rep1

description: Library name: A549_OxPt_UBF_ChIP-rep1


title: A549 cells, oxaliplatin, Pol I (ChIP), rep1

description: Library name: A549_OxPt_RPA194_ChIP-rep1


title: KvPC_SMAD4_KO_SITTB7


title: A549 cells, oxaliplatin, (Input), rep1

description: Library name: A549_OxPt_Input-rep1


title: A549 cells, control, mock IgG (ChIP), rep1

description: Library name: A549_Ctrl_IgG_ChIP-rep1


title: MCAO-3

city: Shijiazhuang

first: xiao

last: zhang

address: No. 215, West Heping Road, Xinhua District, Shijiazhuang

department: Department of Neurology

institute: Second Hospital of Hebei Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text filesinclude Countand FPKMvalues.

source_name: brain

growth_protocol: Healthy adult male C57BL/6 mice (SPF, body weight 23.0-26.0 g, age 8-12 weeks, RRID: IMSR_CRL:27) were performed focal cerebral infarction.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The AGNHW group received AGNHW by gavage at a dose of 450 mg/kg/d, which was equivalent to the human dose of 3 g/60 kg/d according to the Meeh-Rubner equation. The treatment started at 1 h after surgery and continued once a day until sampling. The MCAO group received the same volume of 0.9% saline solution by gavage.

value: brain

tag: condition

value: distal middle cerebral artery occlusion

value: saline

tag: group

value: control

tag: time point

value: male

tag: age

value: adult


title: MCAO-4

tag: tissue


title: MCAO-2


title: A549 cells, control, UBF (ChIP), rep1

description: Library name: A549_Ctrl_UBF_ChIP-rep1

tag: cell line

value: Untreated


title: MCAO-1


title: KvPC_SMAD4_KO_SITTA7

tag: genotype


title: eml12_rep3

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, then transplanted into soil and continued to grow up to 20 days, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 20-day-old Arabidopsis plants with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: seedlings


title: gte4-eml12_rep2


title: gte4-eml12_rep1


title: A549 cells, control, (Input), rep1

description: Library name: A549_Ctrl_Input-rep1

value: Lung

tag: cell type

value: epithelial cells


title: AGNHW-4

value: AGNHW

value: treatment


title: A549 cells, control, Pol I (ChIP), rep1

description: Library name: A549_Ctrl_RPA194_ChIP-rep1


title: gte4_rep3


title: AGNHW-3


title: eml12_rep2


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/- FANCM-/-_dTAG-SMARCAL1-dTAG13

city: toronto

first: Sumin

last: Feng

address: 600 University Avenue

country: Canada

institute: The Lunenfeld-Tanenbaum Research Institute

data_processing:
Adapter trimming and quality preprocessing with cutadapt (v4.5), with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25 -a AGATCGGAAGAG -A AGATCGGAAGAG
Align to genome with bowtie2 (v2.5.0) using parameters -N 1 -L 32
Aligned files sorted, and subset to only keep read one and exclude ENCODE blacklist regions using samtools (v1.20)
Spike in normalization was done by subsampling bam files with samtools (v1.20) using view -s 42. as seed for the spike in factors determined by readcount per sample at a consensus peak set.  The consensus peaks were determined through MACS3 (v3.0.0b3) callpeak (--keep-dup all --nomodel --nolambda -p 1e-5) and bedtools (v2.31.0) intersect
Double stranded breaks were identified by comparing strand separated peaks for each sample from MACS3 (v3.0.0b3) callpeak output using paramters --keep-dup all --nomodel --nolambda -p 1e-5.
bedtools (v2.31.0) intersect was used to compare peak bed files, bamtobed and genomecov were used to convert bam files to bedgraph files
Bedgraph files were converted to bigwigs using the UCSC binary bedGraphToBigWig
Assembly: GRCh38 with spike in GRCg6a
Supplementary files format and content: Bigwig file of genomic coverage

extract_protocol:
Biotinylated DNA fragments were purified using streptavidin beads (Invitrogen, 65002).
DNA library for END-seq was prepared with NEBNext UltraTM II DNA Library Prep Kit for Illumina (NEB, E7645S)

value: retinal pigment epithelial


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/- FANCM-/-_dTAG-SMARCAL1-DMSO

value: DMSO


title: gte4_rep1


title: WT_rep3

value: wild type


title: AGNHW-2


title: eml12_rep1


title: AGNHW-1


title: gte4_rep2


title: WT_rep1


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/-_dTAG-SMARCAL1-DMSO


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/-_dTAG-SMARCAL1-dTAG13


title: Thapsigargin 2h N=3

city: Indianapolis

first: Michael

middle: A

last: Kalwat

state: IN

address: 1210 Waterway Blvd Suite 2000

department: Lilly Diabetes Center of Excellence

institute: Indiana Biosciences Research Institute

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC mm10
Supplementary_files_format_and_content: processed data is a combined Excel table. Sheet 1 contains the mapping statistics. Sheet 2 contains Gene identifier information, log2(FPKM), TPM, and raw counts for all samples.

source_name: MIN6 beta cells

growth_protocol: Mouse MIN6 beta cells were cultured in 12 well dishes in complete medium (DMEM containin 25mM glucose, 10% FBS, 50uM beta-mercaptoethanol, antibiotics).

extract_protocol:
RNA extraction was done with Invitrogen Purelink RNA mini kit with on-column DNAse digestion.
KAPA RNA Hyperprep Kit (KK8581) and QIAseq FastSelect HMR rRNA Removal Kit.

treatment_protocol: Cells were treated with DMSO (0.1%), SW016789 (5uM), or thapsigargin (100nM) for 0, 1, 2, 6, and 24 h. Treatment addition times were staggered such that all samples were collected at the same time at the end of the experiment.

value: insulinoma

value: thapsigargin

tag: time (h)


title: IP_GTE4-WT_FLAG_rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
ChIP-enriched peaks were called uing MACS2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with FLAG antibodies.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: gte4 complemented with 1305-GTE4-FLAG construct


title: Thapsigargin 6h N=3


title: Thapsigargin 24h N=3


title: IP_GTE4-DEL-EID_FLAG_rep2

value: gte4 complemented with 1305-GTE4-{delta}EID-FLAG construct


title: IP_GTE4-DEL-EID_FLAG_rep1


title: SAS clells AD conditons siDsg3

city: Ichikawa-shi

first: junichirou

last: inada

state: Chiba

department: Department of Oral Oncology, Oral and Maxillofacial Surgery

institute: Tokyo Dental College

data_processing:
We conducted 150 base-length paired-end sequencing analysis using the NovaSeq 6000. The raw data obtained was then converted into FASTQ file format using the accompanying software. (NovaSeq Control Software ver1.7.5, Real Time Analysis (RTA) ver3.4.4, bcl2fastq2 ver2.20). Adapter sequences were not removed.
The read sequences obtained from the sequencing analysis were mapped to the reference genome sequence. Based on the positional information obtained from the mapping and the gene definition file, expression levels at the gene and transcript levels were calculated, and annotation information was added. The analysis of known genes was performed using the software’s default parameters. (DRAGEN Bio-IT Platform ver3.7.5)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Oral squamous cell carsinoma cell lines

growth_protocol: Cell lines were maintained in Dulbecco's Modified Eagle's Medium/Nutrient Mixture F-12 Ham with L-glutamine (DMEM/F12) (Sigma-Aldrich, St. Louis, MO) suspending 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA) and 1% penicillin/streptomycin (Thermo Fisher Scientific) at 37°C in a humidified atmosphere with 5% CO2. Cell lines, under AD condition were maintained in 100mm Nunc EasYDish (Thermo Fisher Scientific), under AID conditions were maintained in EZ-BindShut II (IWAKI) 6well plate.

extract_protocol:
Total RNA was extracted from the OSCC cell lines using RNeasy Micro Kit (Qiagen, Hilden, Germany). First-strand cDNA was synthesized according to the manufacturer’s protocol of PrimerScript RT Reagent Kit with gDNA Eraser (Takara, Shiga, Japan).
The cDNA library preparation was performed SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) and Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: Knockdown were performed Dsg3 Silencer®Select Pre-designed siRNA (s4327), and Silencer Select Negative Control #1 siRNA (Cat＃4390843) which were purchased from Thermo Fisher Scientific. These siRNA (concentration of 10µM) were transfected using Lipofectamine RNAiMAX (Themo Fisher Scientific). The transfection according to the manufacture’s protocol. After transfection, 48h incubation, total RNA were extracted.

value: Oral squamous cell carsinoma cell lines

value: Dsg3 knockdown


title: SAS clells AID conditons control

value: WT


title: IP_GTE4-WT_FLAG_rep1


title: IP_EML2-in-gte4_FLAG_rep2

value: 1305-EML2-FLAG transformed plants (in gte4)


title: Thapsigargin 1h N=3


title: gte4-eml12_rep3


title: SAS clells AD conditons control


title: IP_EML2-in-WT_FLAG_rep2

value: 1305-EML2-FLAG transformed plants (in col-0)


title: SW016789 24h N=3


title: WT_rep2

value: seedlings


title: IP_EML2-in-gte4_FLAG_rep1


title: IP_EML2-in-WT_FLAG_rep1


title: SW016789 6h N=3


title: 7ly clells AID conditons control


title: IP_GTE4-YN-AA_FLAG_rep1

value: gte4 complemented with 1305-GTE4-YN-AA-FLAG construct


title: IP_GTE4-in-eml12_FLAG_rep2

value: 1305-GTE4-FLAG transformed plants (in eml1/2)


title: SW016789 2h N=3


title: SAS clells AID conditons siDsg3


title: IP_GTE4-YN-AA_FLAG_rep2


title: IP_GTE4-in-eml12_FLAG_rep1


title: IP_GTE4-in-WT_FLAG_rep2

value: 1305-GTE4-FLAG transformed plants (in col-0)


title: 7ly clells AD conditons siDsg3


title: IP_GTE4-in-WT_FLAG_rep1


title: SW016789 1h N=3


title: Input_GTE4-YN-AA_FLAG

value: input


title: 7ly clells AD conditons control


title: DMSO 6h N=3


title: Input_EML2-in-gte4_FLAG


title: DMSO 24h N=3


title: 7p clells AID conditons siDsg3


title: Input_GTE4-in-eml12_FLAG


title: 7p clells AID conditons control


title: 7ly clells AID conditons siDsg3


title: DMSO 2h N=3


title: 7p clells AD conditons siDsg3


title: DMSO 1h N=3


title: Input_GTE4-in-WT_FLAG


title: SHR3

city: Nanjing

first: Jiaochen

last: Luan

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

description: Library name: Sample 6

data_processing:
Reads were  filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release106
Supplementary files format and content: text files include raw counts from each sample
Supplementary files format and content: text files include FPKM from each sample

organism: Rattus norvegicus

source_name: penile cavernous tissue

extract_protocol:
Total RNA was extracted from rat penile cavernous tissues with TRIzol reagent (Invitrogen, Waltham, MA, USA)
RNA-seq

value: penile cavernous tissue

value: spontaneously hypertensive rats (SHR)


title: SHR2

description: Library name: Sample 5


title: SHR1

description: Library name: Sample 4


title: Baseline 0h N=3

value: not treated


title: 7p clells AD conditons control


title: Norm3

description: Library name: Sample 3

value: normal


title: Multiple Myeloma Plasmacells, S20

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
Sequence reads were trimmed using Trimmomatic (v0.39)
Trimmed sequence reads were aligned using Tophat 2.1.1
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Multiple Myeloma Plasmacells

growth_protocol: CD138-positive tumoral plasma cells were purified through an immunomagnetic procedure and immediately frozen as a dry pellet. Following this, RNA was extracted for RNA sequencing analysis.

extract_protocol:
RNA was extracted with the Qiagen miRNeasy advanced cell/tissue kit, quality controlled using the TapeStation system (Agilent) and quantity controlled with the NanoDrop system (Invitrogen).
Ribosomal RNA depletion was done with RiboCop depletion kit (Lexogen) and RNA-seq libraries were produced using the CORALL total RNA seq Library Prep kit (Lexogen) following manufacturer's protocols.

treatment_protocol: No cell treatment

value: Multiple Myeloma Plasmacells


title: Thapsigargin 24h N=2

value: insulinoma

value: thapsigargin


title: Norm1

description: Library name: Sample 1


title: Monocytes-derived Macrophages M2-Day 7 Replicate 4

city: Chicago

first: Afsar

middle: Raza

last: Naqvi

state: Illinois

address: 801 S Pauline

department: Periodontics

institute: University of Illinois

description:
Library name: Group H_FPKM.M2_Day7_4
FPKM.M2_Day7_4
Group H
Total RNA-seq

data_processing:
Transcripts Assembly: Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Tophat2 to map reads to the genome of Homo sapiens (Version: GRCh38). The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from 37 samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie and Ballgown were used to estimate the expression levels of all transcripts.
lncRNA identification: First, transcripts that overlapped with known mRNAs, known lncRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts with class code (I, j, o, u, x) were considered as lncRNAs.
Different expression analysis of transcripts: StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown.
Target gene prediction and functional analysis of lncRNAs: To explore the function of lncRNAs, we predicted the cis-target genes of lncRNAs. lncRNAs may play a cis role acting on neighboring target genes. In this study, coding genes in 100,000 upstream and downstream were selected by perl script. Then, we showed functional analysis of the target genes for lncRNAs by using the scripts in house. Signiﬁcance was expressed as a p value < 0.05.
Localization of lncRNAs on genome: Two diagrams were generated to show the localization and abundance of lncRNAs in genome using the program Circos. One diagram showed lncRNA expression level in different samples. The lncRNAs in the other diagram were subdivided into five categories according to their class code generated by StringTie: (i) a transfrag falling entirely within a reference intron (intronic); (j) potentially novel isoform or fragment at least one splice junction is shared with a reference transcript; (o) generic exonic overlap with a reference transcript; (u) unknown, intergenic transcript (intergenic); (x) Exonic overlap with reference on the opposite strand (antisense).
Assembly: GRCh38
Supplementary files format and content: Processed_data_macrophages_LncRNAs.xlsx: Excel file

source_name: Healthy buffy coats

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribo-minus RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the pair-end 2×150bp sequencing on an Illumina Hiseq 4000 platform housed in the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.

value: Healthy buffy coats

value: Monocytes-derived macrophages M2

value: Day 7


title: Input_EML2-in-WT_FLAG


title: Norm2

description: Library name: Sample 2


title: Input_GTE4-WT_FLAG

value: gte4 complemented with 1305-GTE4-FLAG construct


title: Monocytes-derived Macrophages M2-Day 7 Replicate 3

description:
Library name: Group H_FPKM.M2_Day7_3
FPKM.M2_Day7_3
Group H
Total RNA-seq


title: Monocytes-derived Macrophages M2-Day 5 Replicate 4

description:
Library name: Group G_FPKM.M2_Day5_4
FPKM.M2_Day5_4
Group G
Total RNA-seq

value: Day 5


title: Thapsigargin 6h N=2


title: Multiple Myeloma Plasmacells, S18


title: Thapsigargin 1h N=2


title: Monocytes-derived Macrophages M2-Day 7 Replicate 1

description:
Library name: Group H_FPKM.M2_Day7_1
FPKM.M2_Day7_1
Group H
Total RNA-seq


title: Multiple Myeloma Plasmacells, S19


title: Multiple Myeloma Plasmacells, S17


title: Multiple Myeloma Plasmacells, S16


title: Monocytes-derived Macrophages M2-Day 5 Replicate 3

description:
Library name: Group G_FPKM.M2_Day5_3
FPKM.M2_Day5_3
Group G
Total RNA-seq


title: Thapsigargin 2h N=2


title: Monocytes-derived Macrophages M2-Day 5 Replicate 2

description:
Library name: Group G_FPKM.M2_Day5_2
FPKM.M2_Day5_2
Group G
Total RNA-seq


title: Input_GTE4-DEL-EID_FLAG

value: seedlings

value: gte4 complemented with 1305-GTE4-{delta}EID-FLAG construct


title: Monocytes-derived Macrophages M2-Day 5 Replicate 1

description:
Library name: Group G_FPKM.M2_Day5_1
FPKM.M2_Day5_1
Group G
Total RNA-seq


title: Monocytes-derived Macrophages M2-Day 3 Replicate 4

description:
Library name: Group F_FPKM.M2_Day3_4
FPKM.M2_Day3_4
Group F
Total RNA-seq

value: Day 3


title: Multiple Myeloma Plasmacells, S15


title: SW016789 24h N=2


title: SW016789 6h N=2


title: Monocytes-derived Macrophages M2-Day 3 Replicate 3

description:
Library name: Group F_FPKM.M2_Day3_3
FPKM.M2_Day3_3
Group F
Total RNA-seq


title: Monocytes-derived Macrophages M2-Day 3 Replicate 2

description:
Library name: Group F_FPKM.M2_Day3_2
FPKM.M2_Day3_2
Group F
Total RNA-seq


title: Multiple Myeloma Plasmacells, S14


title: Monocytes-derived Macrophages M2-Day 3 Replicate 1

description:
Library name: Group F_FPKM.M2_Day3_1
FPKM.M2_Day3_1
Group F
Total RNA-seq


title: Multiple Myeloma Plasmacells, S13


title: Monocytes-derived Macrophages M2-Day 7 Replicate 2

description:
Library name: Group H_FPKM.M2_Day7_2
FPKM.M2_Day7_2
Group H
Total RNA-seq


title: SW016789 2h N=2


title: Monocytes-derived Macrophages M2-18h Replicate 3

description:
Library name: Group E_FPKM.M2_18h_3
FPKM.M2_18h_3
Group E
Total RNA-seq


title: SW016789 1h N=2


title: DMSO 24h N=2

value: DMSO


title: Monocytes-derived Macrophages M2-18h Replicate 1

description:
Library name: Group E_FPKM.M2_18h_1
FPKM.M2_18h_1
Group E
Total RNA-seq


title: Monocytes-derived Macrophages M2-18h Replicate 2

description:
Library name: Group E_FPKM.M2_18h_2
FPKM.M2_18h_2
Group E
Total RNA-seq


title: Multiple Myeloma Plasmacells, S12


title: Monocytes-derived Macrophages M1-Day 7 Replicate 4

description:
Library name: Group D_FPKM.M1_Day7_4
FPKM.M1_Day7_4
Group D
Total RNA-seq

value: Monocytes-derived macrophages M1


title: Multiple Myeloma Plasmacells, S11


title: DMSO 6h N=2


title: DMSO 2h N=2


title: Multiple Myeloma Plasmacells, S10


title: Monocytes-derived Macrophages M1-Day 7 Replicate 3

description:
Library name: Group D_FPKM.M1_Day7_3
FPKM.M1_Day7_3
Group D
Total RNA-seq


title: Monocytes-derived Macrophages M1-Day 7 Replicate 1

description:
Library name: Group D_FPKM.M1_Day7_1
FPKM.M1_Day7_1
Group D
Total RNA-seq


title: Monocytes-derived Macrophages M1-Day 5 Replicate 5

description:
Library name: Group C_FPKM.M1_Day5_5
FPKM.M1_Day5_5
Group C
Total RNA-seq


title: DMSO 1h N=2


title: Monocytes-derived Macrophages M1-Day 5 Replicate 4

description:
Library name: Group C_FPKM.M1_Day5_4
FPKM.M1_Day5_4
Group C
Total RNA-seq


title: Monocytes-derived Macrophages M1-Day 5 Replicate 3

description:
Library name: Group C_FPKM.M1_Day5_3
FPKM.M1_Day5_3
Group C
Total RNA-seq


title: Monocytes-derived Macrophages M1-Day 5 Replicate 2

description:
Library name: Group C_FPKM.M1_Day5_2
FPKM.M1_Day5_2
Group C
Total RNA-seq


title: Baseline 0h N=2


title: Multiple Myeloma Plasmacells, S8


title: Monocytes-derived Macrophages M2-18h Replicate 4

description:
Library name: Group E_FPKM.M2_18h_4
FPKM.M2_18h_4
Group E
Total RNA-seq


title: Multiple Myeloma Plasmacells, S7


title: Thapsigargin 24h N=1


title: Monocytes-derived Macrophages M1-Day 5 Replicate 1

description:
Library name: Group C_FPKM.M1_Day5_1
FPKM.M1_Day5_1
Group C
Total RNA-seq


title: Multiple Myeloma Plasmacells, S6


title: Thapsigargin 6h N=1


title: RPE1-hTERT TP53-/- PACKO Cas9 HLTF-/- T18_B

data_processing:
Count tables of sgRNA created from fastq files using mageck's (v0.5.9.5) count command
Gene essentiality scores calculated as median of 10 iterations of Bagel2 (v2.115), and from CrisprCountsAnalysis (CCA) using default parameters
Custom R script to plot Bagel and CCA results (scatter_bagel_cca_SF202306.R)
Assembly: Toronto KnockOut (TKO) CRISPR Library - Version 3
Supplementary files format and content: XML-based file format xlsx file includes readcount for each sample

extract_protocol:
DNA was harvested by QIAamp Blood Maxi Kit (QIAGEN)
Genome-integrated sgRNA sequences were amplified by PCR using Q5 Mastermix (NEB Next UltraII, New Endland Biolabs, M0544S). i5 and i7 multiplexing barcodes were introduced in a second round of PCR
CRISPR screens

value: retinal pigment epithelial

value: NO


title: RPE1-hTERT TP53-/- PACKO Cas9 WT

data_processing:
Process fastq files for quality and adapters using fastp (v 0.23.4)
Align to genome using STAR (2.7.11a), parameter SortedByCoordinate
Merge replicates together with samtools (v1.20) merge
Convert to bedgraph with bedtools (v2.31.0) bamtobed and genomecov functions
Convert bedgraph to bigwig using UCSC binary bedGraphToBigWig
Assembly: GRCh38
Supplementary files format and content: BigWig file with genomic coverage

extract_protocol:
RNA was harvested by Direct-zol RNA miniprep (Zymo Research)
RNA library for RNA-seq was prepared with Illumina TruSeq Stranded mRNA Library Preparation Kit

value: RPE1-hTERT TP53-/- PACKO Cas9 WT


title: Monocytes-derived Macrophages M1-Day 3 Replicate 5

description:
Library name: Group B_FPKM.M1_Day3_5
FPKM.M1_Day3_5
Group B
Total RNA-seq


title: Monocytes-derived Macrophages M1-Day 3 Replicate 4

description:
Library name: Group B_FPKM.M1_Day3_4
FPKM.M1_Day3_4
Group B
Total RNA-seq


title: Monocytes-derived Macrophages M1-Day 7 Replicate 2

description:
Library name: Group D_FPKM.M1_Day7_2
FPKM.M1_Day7_2
Group D
Total RNA-seq


title: RPE1-hTERT TP53-/- PACKO Cas9 HLTF-/- T0


title: Thapsigargin 2h N=1


title: Multiple Myeloma Plasmacells, S9


title: Thapsigargin 1h N=1


title: Multiple Myeloma Plasmacells, S5


title: Multiple Myeloma Plasmacells, S4


title: Monocytes-derived Macrophages M1-Day 3 Replicate 3

description:
Library name: Group B_FPKM.M1_Day3_3
FPKM.M1_Day3_3
Group B
Total RNA-seq


title: Multiple Myeloma Plasmacells, S3


title: RPE1-hTERT TP53-/- PACKO Cas9 ZRANB3-/- T18_B


title: SW016789 24h N=1


title: Monocytes-derived Macrophages M1-Day 3 Replicate 2

description:
Library name: Group B_FPKM.M1_Day3_2
FPKM.M1_Day3_2
Group B
Total RNA-seq