title: AMO-BZB cells, shMFF - 2

description: Library name: shMFF_sample2


title: CH12F3_AID-KO_Tazemetostat_3

status: Public on Nov 18 2025

type: SRA

city: Boston

first: Roberto

last: Chiarle

state: Ma

address: Longwood 333

country: USA

institute: Boston Childrens Hospital

description:
PE75
CH12F3_AID-KO_Tazemetostat.bw
CH12F3_AID-KO_Tazemetostat.bedgraph

library_source: other

data_processing:
The adapter was removed using cutadapt software
Duplicates were removed using Picard software
Index and alignment was performed using Bowtie software --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 20
Assembly: GRCm37/mm9
Supplementary files format and content: Bigwig
Supplementary files format and content: Bedgraph
Library strategy: Cut&Tag

molecule: other

organism: Mus musculus

growth_protocol: Cells were cultured at 37 °C with 5% CO2

extract_protocol:
The library preparation was performed with the CUT&Tag-IT™ Assay Kit (Active Motif, cat. no. 53160).
The CUT&Tag for H3K27me3 libraries were sequenced through Illumina MiSeq (PE75)

treatment_protocol: CUT&Tag for H3K27me3 libraries were prepared from CH12F3 AID-deficient cells stimulated with anti-CD40–IL-4–TGF-β for 24 h

tag: cell line

tag: cell type

value: Mouse B-lymphoma cells

tag: genotype

value: AID-KO

tag: treatment

value: anti-CD40–IL-4–TGF-Beta + tazemetostat


title: N2, ptr-23, day 8, early adult, replicate 3

city: Durham

first: Ivan

last: Falsztyn

state: NC

address: French Science Center

department: Biology

institute: Duke University

description: Library name: N2_ptr-23_rep4_S21_L001_R1_001.fastq

library_source: transcriptomic

data_processing:
WS273 was used in mapping and analysis
bowtie2-2.3.3.1-linux-x86_64 was used to map paired-end reads (bowtie2 -p 2 -k 1 -S)
HTSeq python-htseq 0.6.1p1-4build1 (amd64 binary) in ubuntu bionic was used to count reads
Assembly: WS273
Supplementary files format and content: COUNTS file with raw counts for each sample

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Early adult, hermaphrodite, whole animal

growth_protocol: L1 larvae were starved in virgin s-basal medium for 8 days at 20°C. Arrested larvae were plated onto the indicated food source (RNAi) and grown for 68 hours prior to collection.

extract_protocol:
100 μL of acid-washed sand and 1 mL of TRIzol were added to frozen worm pellets, and the tubes were vortexed vigorously for 10 minutes to homogenize samples. 200 μL of phenol-chloroform was added, and the mixture was vigorously vortexed for an additional 3 minutes. Tubes were centrifuged for 3 minutes at 21,000 rpm. A p200 micropipette was used to extract the aqueous layer, which was transferred to a new 1.5 mL Eppendorf tube and mixed with 500 μL of isopropanol. The mixture was incubated for 8 minutes at room temperature followed by 2 minutes on ice. Tubes were subsequently centrifuged for 10 minutes at 21,000 rpm. RNA pellets were washed with 75% ethanol twice, after which they were allowed to air dry prior to resuspension in 10 μL of water.
Libraries were prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs #E7775) starting with 1 μg of total RNA per sample as input and seven cycles of PCR.

treatment_protocol: 15 µL of the indicated RNAi strain in E. coli HT115 was transferred and spread  onto nematode growth medium plates with Carbenicillin (50 mg/ml) and IPTG (1 mM) and incubated overnight at room temperature

tag: tissue

value: wild type

value: ptr-23 RNAi


title: N2, empty vector, day 8, early adult, replicate 1

description: Library name: N2_ev_rep2_S1_L001_R1_001.fastq

value: Early adult, hermaphrodite, whole animal

value: empty vector


title: N2, empty vector, day 8, early adult, replicate 2

description: Library name: N2_ev_rep3_S9_L001_R1_001.fastq


title: Dauer Day1, exit 6h, sample 2

city: Cologne

first: Walter

last: Sandt

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD

description: Library name: D1.6.2

data_processing:
fastp processing followed by salmon alignment
Assembly: caenorhabditis_elegans.PRJNA13758.WBPS15.mRNA_transcripts.fa caenorhabditis_elegans.PRJNA13758.WBPS15.genomic.fa (decoy)
Supplementary files format and content: raw_counts.csv

source_name: Whole worm

extract_protocol:
Each condition contained three biological replicates of 8000 worms, collected in ice-cold 1x M9 buffer from plates seeded with OP50. The samples were washed three times with 1x M9 buffer, resuspended in Trizol (Invitrogen) and 0.7 mm zirconia beads (Roth), and quick-frozen in liquid nitrogen at -80°C until RNA extraction was performed. The samples were disrupted using a Precellys24 homogenizer (Bertin) and 1-Bromo-3-chloropane (Sigma-Aldrich) was added for phase separation.
The purification of RNA was performed using the RNeasy Mini Kit (Qiagen) according to the provided instructions. The isolated RNA was eluted in RNase-free H2O and quantified using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific).

value: Whole worm

value: daf-2 constitutive mutant of N2 strain

value: Dauer Day1, exit 6h


title: AMO-BZB cells, SCR - 2

city: Catanzaro

first: Claudia

last: Veneziano

address: Viale Europa, Località Germaneto

department: Department of Experimental and Clinical Medicine

country: Italy

institute: "Magna Graecia" University of Catanzaro

description: Library name: SCR_sample2

data_processing:
Torrent Suite software v5.14.0 was used to align and process the raw sequences. Output normalized counts (in read per milion) were generated as .chp files.
Assembly: hg19
Supplementary files format and content: .chp file for each Sample

organism: Homo sapiens

source_name: AMO-BZB

growth_protocol: H929 MM cells, stably overexpressing MFF or an empty vector as a control, were collected and immediately resuspended in TRIzol Reagent, followed by RNA extraction for RNA sequencing analysis. Similarly, AMO-BZB MM cells, stably silenced for MFF or a scrambled control, were collected, resuspended in TRIzol Reagent, and RNA was extracted for RNA sequencing analysis.

extract_protocol:
RNA was extracted with the fenol/chloroform method, quality and quantity controlled with the NanoDrop system (Invitrogen).
Libraries preparation was manually performed using the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel, according to the Ion AmpliSeq Library Kit Plus.

treatment_protocol: H929 MM cells were stably transduced with lentiviral vectors to overexpress MFF or an empty vector as a control. AMO-BZB MM cells were stably transduced with lentiviral vectors to silence MFF or a scrambled control. After positive selection using puromycin, the silencing and the overexpression of MFF were evaluated.

value: AMO-BZB

value: Multiple Myeloma plasma cells

value: SCR


title: CH12F3_AID-KO_Tazemetostat_2


title: MDA-MB-231, SCUBE3 Knockdown, rep2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: shSCUBE3_2

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 algorithm (v2.0.8b)
gene count measurements were obtained using HTSeq algorithm using refseq annotation
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: polyA RNA

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplented with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen, Cat#74004) and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 50bp single-read sequencing protocol.

treatment_protocol: MDA-MB-231 cells were transfected with lentivirus containing human shRNA (or scrambled shRNA) plasmids for SCUBE3. Transfected cells were then selected with Puromycin for a week and checked for expression of SCUBE3 by western blots.

tag: strain

value: Human

value: Breast cancer

value: transfected with lentivirus containing human shRNA plasmids for SCUBE3


title: MDA-MB-231, SCUBE3 Knockdown, rep3

description: Library name: shSCUBE3_3


title: CH12F3_AID-KO_DMSO-2

data_processing:
GEAT_docker(https://github.com/alessandriLuca/HTGTS_alignment) default parameters
Assembly: mm9
Supplementary files format and content: bedfiles tab separated
Library strategy: LAM-HTGTS

extract_protocol:
The library preparation was performed as previously described in Zhang, X. et al, Nature 575, 385-389 (2019).
12-16 samples were pooled and sequenced through Illumina MiSeq (PE250) by the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

treatment_protocol: LAM-HTGTS libraries were prepared from different CH12F3 mutants stimulated with anti-CD40–IL-4–TGF-β for 72 h

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: AMO-BZB cells, SCR - 1

description: Library name: SCR_sample1


title: Dauer Day1, exit 6h, sample 1

description: Library name: D1.6.1


title: CH12F3_AID-KO_Tazemetostat_1

value: Mouse B-lymphoma cells


title: MDA-MB-231, SCUBE3 Knockdown, rep1

description: Library name: shSCUBE3_1


title: CH12F3_AID-KO_Valemetostat_3

description:
PE75
CH12F3_AID-KO_Valemetostat.bw
CH12F3_AID-KO_Valemetostat.bedgraph

value: AID-KO

value: anti-CD40–IL-4–TGF-Beta + valemetostat


title: H929 cells, overexpressing MFF - 2

description: Library name: H929_OE_MFF_sample2

value: MFF OVEREXPRESSION


title: MDA-MB-231, scramble shRNA, rep3

description: Library name: Scramble_3

value: Scramble control


title: CH12F3_AID-KO_DMSO_2

description:
PE75
CH12F3_AID-KO_DMSO.bw
CH12F3_AID-KO_DMSO.bedgraph


title: Dauer Day1, exit 0h, sample 2

description: Library name: D1.0.2

value: Dauer Day1, exit 0h


title: CH12F3_AID-KO_DMSO_3


title: H929 cells, overexpressing MFF - 1

description: Library name: H929_OE_MFF_sample1


title: MDA-MB-231, scramble shRNA, rep2

description: Library name: Scramble_2


title: H929 cells, empty vector - 2

description: Library name: H929_EV_sample2

value: EMPTY VECTOR


title: Dauer Day1, exit 0h, sample 1

description: Library name: D1.0.1

value: Whole worm


title: MDA-MB-231, scramble shRNA, rep1

description: Library name: Scramble_1


title: Liver, CYP7A1, 36

status: Public on Nov 17 2025

city: Los Angeles

first: Thomas

middle: Q

last: de Aguiar Vallim

state: CA

address: MRL 3230/3240 675 Charles E. Young Drive South

department: Cardiology

institute: University of California, Los Angeles

description:
Library name: Liver_Cyp7a1_36
Cyp7a1_36

data_processing:
Technical replicates run across two lanes were concatenated in Mac Terminal.
Merged read files were trimmed for adapter sequences/low-quality sequences using Trim Galore v0.6.10.
Trimmed reads were aligned to the mm10 reference genome using STAR v2.7.11a.
Raw gene counts were generated using featureCounts (Subread v3.6.3).
Genes with low total counts (fewer than 500 across all samples) were retained and normalized using DESeq2's (R v3.6.3) median-of-ratios.
Assembly: mm10
Supplementary files format and content: csv file includes normalized gene counts for each sample

source_name: liver

extract_protocol:
Total RNA was extracted from flash-frozen tissue samples using the RNeasy Mini Kit (Qiagen, Catalog #74104).
mRNA libraries were prepared from 800 ng RNA using the KAPA RNA Hyperprep Kit (KAPA Biosystems, Catalog #KK8541). Adapters used are from KAPA single index adapters (KK8700)

value: liver


title: CH12F3_AID-KO_DMSO_1


title: Liver, CYP7A1, 24

description:
Library name: Liver_Cyp7a1_24
Cyp7a1_24


title: Liver, CYP7A1, 28

description:
Library name: Liver_Cyp7a1_28
Cyp7a1_28


title: Liver, CYP7A1, 5

description:
Library name: Liver_Cyp7a1_5
Cyp7a1_5


title: Liver, CYP7A1, 26

description:
Library name: Liver_Cyp7a1_26
Cyp7a1_26


title: Liver, CYP7A1, 2

description:
Library name: Liver_Cyp7a1_2
Cyp7a1_2


title: Liver, CYP7A1, 19

description:
Library name: Liver_Cyp7a1_19
Cyp7a1_19


title: Liver, CYP7A1, 17

description:
Library name: Liver_Cyp7a1_17
Cyp7a1_17


title: H929 cells, empty vector - 1

description: Library name: H929_EV_sample1


title: Liver, Ctrl, 38

description:
Library name: Liver_Ctrl_38
Control_38

value: Ctrl


title: Liver, Ctrl, 25

description:
Library name: Liver_Ctrl_25
Control_25


title: Liver, Ctrl, 35

description:
Library name: Liver_Ctrl_35
Control_35


title: Liver, Ctrl, 20

description:
Library name: Liver_Ctrl_20
Control_20


title: Liver, Ctrl, 16

description:
Library name: Liver_Ctrl_16
Control_16


title: Liver, Ctrl, 12

description:
Library name: Liver_Ctrl_12
Control_12


title: Dauer Day1, exit 0h, sample 3

description: Library name: D1.0.3

value: daf-2 constitutive mutant of N2 strain


title: Liver, Ctrl, 13

description:
Library name: Liver_Ctrl_13
Control_13


title: Liver, Ctrl, 7

description:
Library name: Liver_Ctrl_7
Control_7


title: dataset3 ld with spike-in rep3

city: GIF SUR YVETTE

first: Qingyi

last: Wang

address: 630 rue noeztlin

country: France

description: Library name: dataset3_spikein_RNA_ld4_rep3

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using Hisat2.2.1 aligner with the following setting "--rna-strandness R"
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Counts reads:Count how many reads map to genomic features with FeatureCounts with the command "featureCounts -F GTF -t exon -g gene_id -a annotation.gff -T 8 -M -O -s 2 -Q 30 -o Count_reads_to_gene.txt input.bams"
Bigwig files were generated using 'bamCoverage' function of deeptools.
As to spike-in RNAseq, the same pipeline was used to map trimmed reads to Drosophila's genome (https://ftp.ensembl.org/pub/release-110/fasta/drosophila_melanogaster/dna/), and get the read counts of Drosophila spike-in genes
Normalization: DESeq2 was used to calculate size factors, and the CATE package was applied to adjust the matrix by removing spike-in variability. Finally, DESeq2 was used again to compute new size factors to further correct the read counts.
Assembly: tair10
Supplementary files format and content: bigwig
Supplementary files format and content: txt files; readcounts table of RNAseq samples.

organism: Arabidopsis thaliana

source_name: 7-day-old planlets

growth_protocol: Seeds were then sown on ½ MS medium, with 1,1g of Murashige and Skoog (MS) medium (Basalt salt Mixture M0221, Duchefa) under long day conditions (16h light) for 7 days

extract_protocol:
NucleoSpin RNA-Plus Kit (Macherey-Nagel) for standard RNA-seq and Trizol extraction for spike-in RNA seq
Libraries were prepared with 2 µg of total RNA thanks to the NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: for standard RNA seq, shoot apices were dissected (30 apices per sample)

value: 7-day-old planlets

value: ld


title: dataset3 ld with spike-in rep1

description: Library name: dataset3_spikein_RNA_ld2_rep1


title: dataset3 Col0 with spike-in rep3

description: Library name: dataset3_spikein_RNA_Col04_rep3


title: pol2a rep2

description: Library name: RNA_abo_rep2

source_name: Shoot apices

value: Shoot apices


title: ld pol2a rep3

description: Library name: RNA_ldabo_rep3

value: ld pol2a


title: pol2a rep1

description: Library name: RNA_abo_rep1


title: dataset3 ld with spike-in rep2

description: Library name: dataset3_spikein_RNA_ld3_rep2


title: dataset3 Col0 with spike-in rep1

description: Library name: dataset3_spikein_RNA_Col02_rep1


title: ld pol2a rep2

description: Library name: RNA_ldabo_rep2


title: ld rep3

description: Library name: RNA_ld_rep3


title: dataset3 Col0 with spike-in rep2

description: Library name: dataset3_spikein_RNA_Col03_rep2


title: Col0 rep2

description: Library name: RNA_Col_rep2


title: Col0 rep1

description: Library name: RNA_Col_rep1


title: ld pol2a rep1

description: Library name: RNA_ldabo_rep1


title: ld rep2

description: Library name: RNA_ld_rep2


title: ld rep1

description: Library name: RNA_ld_rep1


title: dataset2 ld with spike-in rep3

description: Library name: dataset2_RNAseq_spike_ld_3_rep3


title: Col0 rep3

description: Library name: RNA_Col_rep3


title: dataset2 ld pol2a with spike-in rep3

description: Library name: dataset2_RNAseq_spike_ldabo_rep3


title: dataset2 ld pol2a with spike-in rep1

description: Library name: dataset2_RNAseq_spike_ldabo_rep1


title: dataset2 Col0 with spike-in rep3

description: Library name: dataset2_RNAseq_spike_Col_3_rep3


title: dataset2 ld with spike-in rep2

description: Library name: dataset2_RNAseq_spike_ld_2_rep2


title: dataset2 ld with spike-in rep1

description: Library name: dataset2_RNAseq_spike_ld_1_rep1


title: dataset2 pol2a with spike-in rep3

description: Library name: dataset2_RNAseq_spike_abo_3_rep3


title: dataset2 Col0 with spike-in rep1

description: Library name: dataset2_RNAseq_spike_Col_1_rep1


title: dataset2 Col0 with spike-in rep2

description: Library name: dataset2_RNAseq_spike_Col_2_rep2


title: dataset2 pol2a with spike-in rep2

description: Library name: dataset2_RNAseq_spike_abo_2_rep2


title: pol2a rep3

description: Library name: RNA_abo_rep3


title: dataset2 pol2a with spike-in rep1

description: Library name: dataset2_RNAseq_spike_abo_1_rep1


title: dataset1 ld with spike-in rep3

description: Library name: dataset1_RNAseq_spike_ld3_rep3


title: dataset1 ld with spike-in rep1

description: Library name: dataset1_RNAseq_spike_ld1_rep1


title: dataset2 ld pol2a with spike-in rep2

description: Library name: dataset2_RNAseq_spike_ldabo_rep2


title: dataset1 fld with spike-in rep3

description: Library name: dataset1_RNAseq_spike_fld3_rep3

value: fld


title: dataset1 fld with spike-in rep2

description: Library name: dataset1_RNAseq_spike_fld2_rep2


title: dataset1 fld with spike-in rep1

description: Library name: dataset1_RNAseq_spike_fld1_rep1


title: dataset1 Col0 with spike-in rep3

description: Library name: dataset1_RNAseq_spike_Col03_rep3


title: dataset1 Col0 with spike-in rep1

description: Library name: dataset1_RNAseq_spike_Col01_rep1


title: ChIP-seq H3K9ac in ld rep2

description: Library name: IP_ld_K9ac, rep2

library_source: genomic

data_processing:
ChIP-Seq raw reads were mapped to TAIR10 genome assembly using the Chromap software with parameter ‘--preset chip’.
Bigwig files were generated using 'bamCoverage' function of deeptools.
Assembly: tair10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: whole plantlets

growth_protocol: Seeds were then sown on ½ MS medium, with 1,1g of Murashige and Skoog (MS) medium (Basalt salt Mixture M0221, Duchefa) under long day conditions (16h light) for 10 days

extract_protocol:
Chromatin was extracted as described in Huang et al, Nature Com 2023, doi: 10.1038/s41467-023-36227-3
Libraries were then generated using a minimum of 2 ng of DNA with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs)

value: whole plantlets

tag: chip antibody

value: Millipore 07-352


title: input ChIP-seq H3K9ac in WT rep2

description: Library name: input_Col0_K9ac, rep2


title: ChIP-seq H3K9ac in ld rep1

description: Library name: IP_ld_H3K9ac, rep1


title: input ChIP-seq H3K9ac in ld rep1

description: Library name: input_ld_H3K9ac, rep1


title: ChIP-seq RNA polII S5P in ld

description: Library name: ld-IP-S-5

value: Abcam, ab5408


title: ChIP-seq H3K9ac in WT rep2

description: Library name: IP_Col0_K9ac, rep2


title: input ChIP-seq H3K9ac in WT rep1

description: Library name: input_Col0_H3K9ac, rep1


title: ChIP-seq H3K9ac in WT rep1

description: Library name: IP_Col0_H3K9ac, rep1


title: ChIP-seq RNA polII S2P in ld

description: Library name: ld-IP-S-2

value: Abcam, ab238146


title: input for LD ChIPseq rep2

description: Library name: Input_pLD_GFP, rep2

value: ld pLD-LD-GFP


title: LD ChIP seq rep2

description: Library name: pLD-GFP, rep2

value: Abcam, ab290


title: ChIP-seq RNA polII S2P in WT

description: Library name: Col0-IP-S-2


title: ChIP-seq RNA polII S5P in WT

description: Library name: Col0-IP-S-5


title: input for LD ChIPseq rep1

description: Library name: input_pLD_LD-GFP, rep1


title: LD ChIP seq rep1

description: Library name: pLD_LD-GFP, rep1


title: dataset1 ld with spike-in rep2

description: Library name: dataset1_RNAseq_spike_ld2_rep2


title: patient22_csf

type: other

city: Memphis

first: Kyle

middle: S

last: Smith

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

hyb_protocol: Bisulphite converted DNA was amplified and hybridized to human MethylationEPIC BeadChip

scan_protocol: Array were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing:
MethylVerse python package (v0.0.9)
*processed value definition: Average Beta

label: Cy3 and Cy5

source_name: CSF

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from samples using Qiagen Kit according to standard instructions

value: CSF

value: ETMR

tag: sample group


title: patient4_csf


title: patient16_csf


title: patient1_csf


title: patient25_csf


title: patient31_csf


title: patient32_csf


title: patient6_csf


title: dataset1 Col0 with spike-in rep2

description: Library name: dataset1_RNAseq_spike_Col02_rep2


title: patient24_csf


title: patient11_csf


title: input ChIP-seq H3K9ac in ld rep2

description: Library name: input_ld_K9ac, rep2


title: patient23_csf


title: patient29_csf


title: patient15_csf2


title: patient28_csf


title: patient14_csf


title: patient15_csf1


title: patient30_csf


title: patient12_csf


title: patient26_csf


title: patient156

source_name: primary tumor

value: primary tumor

value: Brain tumor patient


title: patient154


title: patient19_csf


title: patient153


title: patient150


title: patient152


title: patient151


title: patient149


title: patient147


title: patient145


title: patient146


title: patient143


title: patient21_csf


title: patient142


title: patient141


title: patient140


title: patient138


title: patient18_csf


title: patient27_csf


title: patient139


title: patient135


title: patient133


title: patient155


title: patient136


title: patient131


title: patient132


title: patient130


title: patient148


title: patient7_csf


title: patient127


title: patient128


title: patient129


title: patient144


title: patient125


title: patient123


title: patient124


title: patient119


title: patient121


title: patient120


title: patient118


title: patient137


title: patient122


title: patient134


title: patient117


title: patient116


title: patient115


title: patient112


title: patient114


title: patient110


title: patient113


title: patient109


title: patient111


title: patient108


title: patient107


title: patient126


title: patient104


title: patient105

value: PXA


title: patient101


title: patient102


title: patient100


title: patient98


title: patient103


title: patient97


title: patient96


title: patient95


title: patient94_2


title: patient94_1


title: patient93


title: patient91


title: patient92


title: patient89


title: patient90


title: patient88


title: patient86


title: patient85


title: patient84


title: patient106


title: patient83


title: patient80


title: patient81


title: patient79


title: patient78


title: patient99


title: patient77


title: patient74


title: patient76


title: patient72


title: patient75


title: patient73


title: patient70


title: patient71


title: patient69


title: patient68


title: patient67


title: patient66


title: patient65


title: patient87


title: patient63


title: patient62


title: patient82


title: patient64


title: patient59


title: patient61


title: patient57


title: patient60


title: patient58


title: patient56


title: patient54


title: patient55


title: patient53


title: patient52


title: patient51


title: patient49


title: patient48


title: patient50


title: patient47


title: patient46


title: patient45


title: patient44


title: patient43


title: patient42


title: patient41


title: patient39


title: patient38


title: patient36


title: patient37


title: patient34


title: patient32


title: patient35


title: patient30


title: patient31


title: patient29


title: patient27


title: patient26


title: patient24


title: patient25


title: patient22


title: patient23


title: patient21


title: patient18


title: patient17

value: MNG


title: patient19


title: patient16


title: patient40


title: patient15


title: patient14


title: patient12


title: patient33


title: patient11


title: patient9

value: GCT


title: patient8


title: patient10


title: patient28


title: patient7


title: patient4


title: patient3


title: patient6


title: patient2


title: D01

city: Bangkok

first: Thanawat

last: Suwatthanarak

address: 2 Wanglang Road, Bangkok-Noi

country: Thailand

institute: Mahidol University

description: Library name: D01

data_processing:
Sequencing reads were demultiplexed and aligned to target probe sequences using the NanoString GeoMx DSP Analysis Suite (v3.1.0.194) following the Human Whole Transcriptome Atlas (WTA) workflow. Raw probe-level counts were subjected to biological-probe quality control and normalization according to manufacturer guidelines. The limit of quantitation (LOQ) was determined from negative control probes, and low-abundance transcripts were filtered accordingly. Normalized expression matrices were generated using Quartile 3 (Q3) and trimmed mean of M-values (TMM) methods. Downstream data processing, principal-component analysis, and differential gene-expression testing were performed in R (standR and DESeq2 packages). Only areas of illumination (AOIs) that passed QC metrics were retained for analysis, and normalized count tables were used for comparative evaluation of FFPE, fresh-frozen, and snap-frozen colorectal-cancer tissues.
Supplementary files format and content: TargetCountMatrix_allSamples.txt
Library strategy: Spatial Transcriptomics

source_name: Colorectal cancer

extract_protocol:
Colorectal cancer (CRC) tissue specimens were collected from a patient with stage IV disease during surgical resection at Siriraj Hospital, Mahidol University, Thailand. Three preservation methods were used: formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF). For FF tissues, specimens were cut into 2–3 mm pieces within 30 minutes of resection and immersed in chilled RNAlater solution. SF tissues were rapidly frozen in liquid nitrogen. FFPE tissues were fixed in formalin and embedded in paraffin according to standard clinical practice. Sections (5 µm) from all tissue types were mounted on Superfrost Plus slides for spatial transcriptomic analysis. RNA integrity was verified (DV200 > 50%) before library preparation. Barcoded oligonucleotides released from defined tissue areas were collected and sequenced on an Illumina NovaSeq 6000 following NanoString GeoMx DSP Human Whole Transcriptome Atlas (WTA) workflow guidelines.
Spatial whole-transcriptome libraries were constructed using the NanoString GeoMx Digital Spatial Profiler (DSP) Human Whole Transcriptome Atlas (WTA) workflow. Tissue sections were hybridized with UV-photocleavable oligonucleotide probes complementary to target mRNA transcripts. Following region-of-interest (ROI) selection, oligonucleotide tags were released from each compartment (PanCK⁺, CD45⁺, and PanCK⁻/CD45⁻) by UV illumination and collected into separate wells. The released barcodes were subjected to PCR amplification and indexing using the GeoMx WTA Library Preparation Kit, following the manufacturer’s protocol. Final libraries were purified, quantified, and quality-checked before sequencing on an Illumina NovaSeq 6000 platform.

value: Colorectal cancer


title: patient20


title: C12

description: Library name: C12


title: C09

description: Library name: C09


title: C11

description: Library name: C11


title: C07

description: Library name: C07


title: C05

description: Library name: C05


title: patient13


title: C04

description: Library name: C04


title: C10

description: Library name: C10


title: C08

description: Library name: C08


title: C03

description: Library name: C03


title: C06

description: Library name: C06


title: C01

description: Library name: C01


title: C02

description: Library name: C02


title: B11

description: Library name: B11


title: B12

description: Library name: B12


title: B08

description: Library name: B08


title: patient5


title: B10

description: Library name: B10


title: B07

description: Library name: B07


title: B06

description: Library name: B06


title: patient1


title: B04

description: Library name: B04


title: B03

description: Library name: B03


title: B05

description: Library name: B05


title: B01

description: Library name: B01


title: B02

description: Library name: B02


title: A12

description: Library name: A12


title: A11

description: Library name: A11


title: A10

description: Library name: A10


title: A09

description: Library name: A09


title: A08

description: Library name: A08


title: A06

description: Library name: A06


title: A04

description: Library name: A04


title: A05

description: Library name: A05


title: A02

description: Library name: A02


title: B09

description: Library name: B09


title: Human lung snRNA-seq sample JN10XHT166

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

description: Library name: JN10XHT166

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using the Cell Ranger pipeline (v7.1, 10x Genomics) to align reads to the human reference genome (GRCh38), generate feature-barcode matrices, and estimate gene expression levels.
Ambient RNA contamination was removed using CellBender v0.2 (fpr = 0.01, epochs = 150, and expected cells provided based on the estimate from the Cell ranger pipeline).
The snRNA-seq data were processed and analyzed using Seurat v5.1. Data were log-normalized using the NormalizeData function, and 2,000 variable genes, excluding antisense and mitochondrial genes, were selected. Gene expression values were scaled while regressing out the percent mitochondrial reads and the number of detected features. A 2% mitochondrial threshold was applied to all cells, except for lymphocytes, for which a 3% threshold was used. Principal Component Analysis (PCA) was performed for dimensionality reduction, and samples were integrated using Harmony (v1.2.0). The Harmony-corrected data were then used to create UMAP embeddings and shared nearest neighbor graphs for Louvain clustering.
DoubletFinder (v2.0) was used to identify doublets computationally, and an iterative clustering approach was applied to remove additional clusters identified as doublets or cellular debris.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz (cell/nucleus barcodes)
Supplementary files format and content: features.tsv.gz (gene annotation)
Supplementary files format and content: matrix.mtx.gz (UMI count matrix in Matrix Market format)
Supplementary files format and content: cell_metadata.tsv (cell/nucleus-level metadata, including cell_barcode, sample_id, nCount_RNA, nFeature_RNA, percent.mt, and cell-type annotations)

molecule: nuclear RNA

source_name: lung

extract_protocol:
Nuclei were isolated from human snap frozen lung tissue using the Chromium10x genomics nuclei isolation kit, per manual. An aliquot of nuclei was stained with 0.4% trypan blue stain and DAPI and subsequently counted with the Thermo Fisher countess II FL. Samples with > 90% viability were used for downstream analysis.
Approximately 20,000 nuclei per sample were loaded onto chip M and processed with the Chromium X controller. Barcoding and DNA (cDNA) library preparation was performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell 3' HT Kit v3.1). Quality of the cDNA was assessed at 2 time points with the Agilent Bioanalyzer High sensitivity DNA chip. The cDNA libraries were sequenced on the Novaseq 6000, using a Hiseq paired end 100bp sequencing configuration, with a read depth of approximately 60,000 reads and 3400 UMI per nuclei.

value: lung


title: A03

description: Library name: A03


title: Human lung snRNA-seq sample JN10XHT165

description: Library name: JN10XHT165


title: Human lung snRNA-seq sample JN10XHT164

description: Library name: JN10XHT164


title: Human lung snRNA-seq sample JN10XHT161

description: Library name: JN10XHT161


title: Human lung snRNA-seq sample JN10XHT163

description: Library name: JN10XHT163


title: Human lung snRNA-seq sample JN10XHT162

description: Library name: JN10XHT162


title: Human lung snRNA-seq sample JN10XHT158

description: Library name: JN10XHT158


title: Human lung snRNA-seq sample JN10XHT160

description: Library name: JN10XHT160


title: Human lung snRNA-seq sample JN10XHT157

description: Library name: JN10XHT157


title: Human lung snRNA-seq sample JN10XHT159

description: Library name: JN10XHT159


title: Human lung snRNA-seq sample JN10XHT156

description: Library name: JN10XHT156


title: Human lung snRNA-seq sample JN10XHT151

description: Library name: JN10XHT151


title: Human lung snRNA-seq sample JN10XHT155

description: Library name: JN10XHT155


title: Human lung snRNA-seq sample JN10XHT152

description: Library name: JN10XHT152


title: Human lung snRNA-seq sample JN10XHT149

description: Library name: JN10XHT149


title: Human lung snRNA-seq sample JN10XHT154

description: Library name: JN10XHT154


title: Human lung snRNA-seq sample JN10XHT153

description: Library name: JN10XHT153


title: A07

description: Library name: A07


title: Human lung snRNA-seq sample JN10XHT148

description: Library name: JN10XHT148


title: Human lung snRNA-seq sample JN10XHT146

description: Library name: JN10XHT146


title: Human lung snRNA-seq sample JN10XHT147

description: Library name: JN10XHT147


title: Human lung snRNA-seq sample JN10XHT145

description: Library name: JN10XHT145


title: Human lung snRNA-seq sample JN10XHT143

description: Library name: JN10XHT143


title: Human lung snRNA-seq sample JN10XHT142

description: Library name: JN10XHT142


title: Human lung snRNA-seq sample JN10XHT141

description: Library name: JN10XHT141


title: Human lung snRNA-seq sample JN10XHT139

description: Library name: JN10XHT139


title: Human lung snRNA-seq sample JN10XHT138

description: Library name: JN10XHT138


title: Human lung snRNA-seq sample JN10XHT137

description: Library name: JN10XHT137


title: Human lung snRNA-seq sample JN10XHT135

description: Library name: JN10XHT135


title: Human lung snRNA-seq sample JN10XHT133

description: Library name: JN10XHT133


title: Human lung snRNA-seq sample JN10XHT136

description: Library name: JN10XHT136


title: Human lung snRNA-seq sample JN10XHT131

description: Library name: JN10XHT131


title: Human lung snRNA-seq sample JN10XHT132

description: Library name: JN10XHT132


title: Human lung snRNA-seq sample JN10XHT130

description: Library name: JN10XHT130


title: Human lung snRNA-seq sample JN10XHT123

description: Library name: JN10XHT123


title: Human lung snRNA-seq sample JN10XHT129

description: Library name: JN10XHT129


title: Human lung snRNA-seq sample JN10XHT125

description: Library name: JN10XHT125


title: Human lung snRNA-seq sample JN10XHT126

description: Library name: JN10XHT126


title: Human lung snRNA-seq sample JN10XHT122

description: Library name: JN10XHT122


title: Human lung snRNA-seq sample JN10XHT121

description: Library name: JN10XHT121


title: Human lung snRNA-seq sample JN10XHT124

description: Library name: JN10XHT124


title: Human lung snRNA-seq sample JN10XHT117

description: Library name: JN10XHT117


title: Human lung snRNA-seq sample JN10XHT120

description: Library name: JN10XHT120


title: Human lung snRNA-seq sample JN10XHT114

description: Library name: JN10XHT114


title: Human lung snRNA-seq sample JN10XHT119

description: Library name: JN10XHT119


title: Human lung snRNA-seq sample JN10XHT115

description: Library name: JN10XHT115


title: Human lung snRNA-seq sample JN10XHT112

description: Library name: JN10XHT112


title: Human lung snRNA-seq sample JN10XHT144

description: Library name: JN10XHT144


title: Human lung snRNA-seq sample JN10XHT113

description: Library name: JN10XHT113


title: Human lung snRNA-seq sample JN10XHT116

description: Library name: JN10XHT116


title: Human lung snRNA-seq sample JN10XHT110

description: Library name: JN10XHT110


title: Human lung snRNA-seq sample JN10XHT111

description: Library name: JN10XHT111


title: Human lung snRNA-seq sample JN10XHT106

description: Library name: JN10XHT106


title: Human lung snRNA-seq sample JN10XHT107

description: Library name: JN10XHT107


title: Human lung snRNA-seq sample JN10XHT105

description: Library name: JN10XHT105


title: Human lung snRNA-seq sample JN10XHT104

description: Library name: JN10XHT104


title: Human lung snRNA-seq sample JN10XHT108

description: Library name: JN10XHT108


title: Human lung snRNA-seq sample JN10XHT101

description: Library name: JN10XHT101


title: Human lung snRNA-seq sample JN10XHT98

description: Library name: JN10XHT98


title: Human lung snRNA-seq sample JN10XHT100

description: Library name: JN10XHT100


title: Human lung snRNA-seq sample JN10XHT99

description: Library name: JN10XHT99


title: Human lung snRNA-seq sample JN10XHT94

description: Library name: JN10XHT94


title: Human lung snRNA-seq sample JN10XHT97

description: Library name: JN10XHT97


title: Human lung snRNA-seq sample JN10XHT95

description: Library name: JN10XHT95


title: Human lung snRNA-seq sample JN10XHT96

description: Library name: JN10XHT96


title: Human lung snRNA-seq sample JN10XHT88

description: Library name: JN10XHT88


title: Human lung snRNA-seq sample JN10XHT92

description: Library name: JN10XHT92


title: Human lung snRNA-seq sample JN10XHT91

description: Library name: JN10XHT91


title: Human lung snRNA-seq sample JN10XHT90

description: Library name: JN10XHT90


title: Human lung snRNA-seq sample JN10XHT87

description: Library name: JN10XHT87


title: Human lung snRNA-seq sample JN10XHT85

description: Library name: JN10XHT85


title: Human lung snRNA-seq sample JN10XHT84

description: Library name: JN10XHT84


title: Human lung snRNA-seq sample JN10XHT82

description: Library name: JN10XHT82


title: Human lung snRNA-seq sample JN10XHT83

description: Library name: JN10XHT83


title: Human lung snRNA-seq sample JN10XHT79

description: Library name: JN10XHT79


title: Human lung snRNA-seq sample JN10XHT81

description: Library name: JN10XHT81


title: Human lung snRNA-seq sample JN10XHT80

description: Library name: JN10XHT80


title: Human lung snRNA-seq sample JN10XHT102

description: Library name: JN10XHT102


title: Human lung snRNA-seq sample JN10XHT77

description: Library name: JN10XHT77


title: Human lung snRNA-seq sample JN10XHT103

description: Library name: JN10XHT103


title: Human lung snRNA-seq sample JN10XHT78

description: Library name: JN10XHT78


title: Human lung snRNA-seq sample JN10XHT76

description: Library name: JN10XHT76


title: Human lung snRNA-seq sample JN10XHT75

description: Library name: JN10XHT75


title: Human lung snRNA-seq sample JN10XHT74

description: Library name: JN10XHT74


title: Human lung snRNA-seq sample JN10XHT70

description: Library name: JN10XHT70


title: Human lung snRNA-seq sample JN10XHT68

description: Library name: JN10XHT68


title: Human lung snRNA-seq sample JN10XHT72

description: Library name: JN10XHT72


title: Human lung snRNA-seq sample JN10XHT86

description: Library name: JN10XHT86


title: Human lung snRNA-seq sample JN10XHT67

description: Library name: JN10XHT67


title: Human lung snRNA-seq sample JN10XHT62

description: Library name: JN10XHT62


title: Human lung snRNA-seq sample JN10XHT64

description: Library name: JN10XHT64


title: Human lung snRNA-seq sample JN10XHT66

description: Library name: JN10XHT66


title: Human lung snRNA-seq sample JN10XHT61

description: Library name: JN10XHT61


title: Human lung snRNA-seq sample JN10XHT65

description: Library name: JN10XHT65


title: Human lung snRNA-seq sample JN10XHT63

description: Library name: JN10XHT63


title: Treat_3

city: Shenzhen

first: Xiaodong

address: Xueyuan Avenue

country: China

institute: Shenzhen University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), and low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: MDA-MB-231 cells

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen). 2 μg total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth Co., Ltd.) following manufacturer's protocols.

value: MDA-MB-231 cells

value: tumor cells

value: WT

value: treated by BN1 for 24 h


title: Human lung snRNA-seq sample JN10XHT59

description: Library name: JN10XHT59


title: Human lung snRNA-seq sample JN10XHT60

description: Library name: JN10XHT60


title: Human lung snRNA-seq sample JN10XHT56

description: Library name: JN10XHT56


title: Human lung snRNA-seq sample JN10XHT55

description: Library name: JN10XHT55


title: Human lung snRNA-seq sample JN10XHT52

description: Library name: JN10XHT52


title: Human lung snRNA-seq sample JN10XHT58

description: Library name: JN10XHT58


title: Human lung snRNA-seq sample JN10XHT54

description: Library name: JN10XHT54


title: Human lung snRNA-seq sample JN10XHT51

description: Library name: JN10XHT51


title: Human lung snRNA-seq sample JN10XHT47

description: Library name: JN10XHT47


title: Human lung snRNA-seq sample JN10XHT48

description: Library name: JN10XHT48


title: Human lung snRNA-seq sample JN10XHT50

description: Library name: JN10XHT50


title: Human lung snRNA-seq sample JN10XHT73

description: Library name: JN10XHT73


title: Human lung snRNA-seq sample JN10XHT69

description: Library name: JN10XHT69


title: Human lung snRNA-seq sample JN10XHT49

description: Library name: JN10XHT49


title: Human lung snRNA-seq sample JN10XHT45

description: Library name: JN10XHT45


title: Human lung snRNA-seq sample JN10XHT46

description: Library name: JN10XHT46


title: Human lung snRNA-seq sample JN10XHT43

description: Library name: JN10XHT43


title: Human lung snRNA-seq sample JN10XHT40

description: Library name: JN10XHT40


title: Human lung snRNA-seq sample JN10XHT44

description: Library name: JN10XHT44


title: Human lung snRNA-seq sample JN10XHT39

description: Library name: JN10XHT39


title: Human lung snRNA-seq sample JN10XHT38

description: Library name: JN10XHT38


title: Human lung snRNA-seq sample JN10XHT35

description: Library name: JN10XHT35


title: Human lung snRNA-seq sample JN10XHT34

description: Library name: JN10XHT34


title: Human lung snRNA-seq sample JN10XHT36

description: Library name: JN10XHT36


title: Human lung snRNA-seq sample JN10XHT32

description: Library name: JN10XHT32


title: Human lung snRNA-seq sample JN10XHT33

description: Library name: JN10XHT33


title: Human lung snRNA-seq sample JN10XHT57

description: Library name: JN10XHT57


title: Human lung snRNA-seq sample JN10XHT31

description: Library name: JN10XHT31


title: Human lung snRNA-seq sample JN10XHT30

description: Library name: JN10XHT30


title: Human lung snRNA-seq sample JN10XHT29

description: Library name: JN10XHT29


title: Human lung snRNA-seq sample JN10XHT28

description: Library name: JN10XHT28


title: Human lung snRNA-seq sample JN10XHT27

description: Library name: JN10XHT27


title: Human lung snRNA-seq sample JN10XHT26

description: Library name: JN10XHT26


title: Human lung snRNA-seq sample JN10XHT19

description: Library name: JN10XHT19


title: Human lung snRNA-seq sample JN10XHT18

description: Library name: JN10XHT18


title: Human lung snRNA-seq sample JN10XHT16

description: Library name: JN10XHT16


title: Human lung snRNA-seq sample JN10XHT17

description: Library name: JN10XHT17


title: Human lung snRNA-seq sample JN10XHT41

description: Library name: JN10XHT41


title: Human lung snRNA-seq sample JN10XHT13

description: Library name: JN10XHT13


title: Human lung snRNA-seq sample JN10XHT10

description: Library name: JN10XHT10


title: Human lung snRNA-seq sample JN10XHT11

description: Library name: JN10XHT11


title: Human lung snRNA-seq sample JN10XHT9

description: Library name: JN10XHT9


title: Human lung snRNA-seq sample JN10XHT37

description: Library name: JN10XHT37


title: Human lung snRNA-seq sample JN10XHT7

description: Library name: JN10XHT7


title: Human lung snRNA-seq sample JN10XHT5

description: Library name: JN10XHT5


title: Human lung snRNA-seq sample JN10XHT6

description: Library name: JN10XHT6


title: Human lung snRNA-seq sample JN10XHT3

description: Library name: JN10XHT3


title: Human lung snRNA-seq sample JN10XHT4

description: Library name: JN10XHT4


title: Human lung snRNA-seq sample JN10XHT1

description: Library name: JN10XHT1


title: Human lung snRNA-seq sample JN10XHT22

description: Library name: JN10XHT22


title: Human lung snRNA-seq sample JN10XHT20

description: Library name: JN10XHT20


title: Human lung snRNA-seq sample JN10XHT21

description: Library name: JN10XHT21


title: MDA-MB-231, Control, bio rep 3

city: Buffalo

first: Jianxin

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description: Library name: MDA-MB-231, Control, bio rep 3

data_processing:
nf-core/rnaseq  version 3.3.
Assembly: GRCh38, GRCm38
Supplementary files format and content: Tab delimited text files, contain raw read counts at isoform level.

source_name: TNBC cell lines

growth_protocol: AT-3 and MDA-MB 231 cells  with RBΔCDK isoform were grown in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic. 4T1 and HCC1806 cells  with RBΔCDK isoform were grown in RPMI 1640 supplemented with 10% FBS and 1% antibiotic-antimycotic.

extract_protocol:
RNA was extracted using Quiagen Rneasy plus mini Kit.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The cells were treated with 0.1% DMSO and Doxycycline (1 μg/mL) up to 48 hours

value: TNBC cell lines

value: Cancer


title: MDA-MB-231, Control, bio rep 2

description: Library name: MDA-MB-231, Control, bio rep 2


title: HCC1806, Dox treated, bio rep 2

description: Library name: HCC1806, Dox treated, bio rep 2


title: MDA-MB-231 Dox treated, bio rep 2

description: Library name: MDA-MB-231 Dox treated, bio rep 2


title: MDA-MB-231, Dox treated, bio rep 1

description: Library name: MDA-MB-231, Dox treated, bio rep 1


title: MDA-MB-231, Control, bio rep 1

description: Library name: MDA-MB-231, Control, bio rep 1


title: HCC1806, Dox treated, bio rep 1

description: Library name: HCC1806, Dox treated, bio rep 1


title: HCC1806, Dox treated, bio rep 4

description: Library name: HCC1806, Dox treated, bio rep 4


title: Human lung snRNA-seq sample JN10XHT23

description: Library name: JN10XHT23


title: HCC1806, Control, bio rep 1

description: Library name: HCC1806, Control, bio rep 1


title: HCC1806, Control, bio rep 3

description: Library name: HCC1806, Control, bio rep 3


title: Human lung snRNA-seq sample JN10XHT14

description: Library name: JN10XHT14


title: HCC1806, Control, bio rep 4

description: Library name: HCC1806, Control, bio rep 4


title: HCC1806, Control, bio rep 2

description: Library name: HCC1806, Control, bio rep 2


title: GSC11 cells, DMSO_3

city: San Diego

first: raghavendra

last: vadla

address: sanford consortium for regenerative medicine, 2880 Torrey Pines Scenic Drive

institute: UCSD

description:
Library name: Sample 30
raw_counts_1.txt
GSC11_DMSO_3

data_processing:
Fastq file quality was ensured with FastQC, and reads were aligned to the hg38 index using STAR. Alignment quality was confirmed by assessing the final STAR logs. Index and bigwig files were generated from the BAM files with samtools and bamCoverage, respectively. Each BAM file was viewed in IGV to assess the quality and features of mapped reads. The Subread package was used to generate count files
Assembly: GRCh38 (GENCODE v39)
Supplementary files format and content: tab-delimited text includes raw counts for each sample

source_name: Brain

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
Novogene sequencing

value: Brain

value: Glioma stem cells

value: DMSO


title: GSC11 cells, GSK620_3

description:
Library name: Sample 33
raw_counts_1.txt
GSC11_GSK620_3


title: GSC11 cells, GSK620_2

description:
Library name: Sample 32
raw_counts_1.txt
GSC11_GSK620_2


title: GSC11 cells, GSK620_1

description:
Library name: Sample 31
raw_counts_1.txt
GSC11_GSK620_1


title: MDA-MB-231, Dox treated, bio rep 3

description: Library name: MDA-MB-231, Dox treated, bio rep 3


title: GSC11 cells, DMSO_2

description:
Library name: Sample 29
raw_counts_1.txt
GSC11_DMSO_2


title: Human lung snRNA-seq sample JN10XHT2

description: Library name: JN10XHT2


title: GSC11 cells, DMSO_1

description:
Library name: Sample 28
raw_counts_1.txt
GSC11_DMSO_1


title: TS576 cell, PTENKO_1

description:
Library name: Sample 25
raw_counts_4.txt
TS576_PTENKO_1

value: TS576 PTENKO

value: PTENKO


title: TS576 cell, PTENKO_3

description:
Library name: Sample 27
raw_counts_4.txt
TS576_PTENKO_3


title: TS576 cell, PTENKO_2

description:
Library name: Sample 26
raw_counts_4.txt
TS576_PTENKO_2


title: TS576 cell, parental_1

description:
Library name: Sample 22
raw_counts_4.txt
TS576_1

value: parental


title: GSC11 cells, BRD2_BD1/2_1

description:
Library name: Sample 19
raw_counts_1.txt
GSC11_BRD2KO+Y113F-Y386F_1


title: GSC11 cells, BRD2_BD2_2

description:
Library name: Sample 17
raw_counts_1.txt
GSC11_BRD2KO+Y386F_2


title: GSC11 cells, BRD2_BD1_2

description:
Library name: Sample 14
raw_counts_1.txt
GSC11_BRD2KO+Y113F_2


title: GSC11 cells, BRD2_WT_3

description:
Library name: Sample 12
raw_counts_1.txt
GSC11_BRD2KO+WT_3


title: GSC11 cells, BRD2_WT_2

description:
Library name: Sample 11
raw_counts_1.txt
GSC11_BRD2KO+WT_2


title: GSC11 cells, RelA K310R_3

description:
Library name: Sample 9
raw_counts_1.txt
GSC11_K310R_3

value: RelA K310R


title: HCC1806, Dox treated, bio rep 3

description: Library name: HCC1806, Dox treated, bio rep 3


title: GSC11 cells, BRD2_BD1/2_3

description:
Library name: Sample 21
raw_counts_1.txt
GSC11_BRD2KO+Y113F-Y386F_3


title: GSC11 cells, BRD2_BD1/2_2

description:
Library name: Sample 20
raw_counts_1.txt
GSC11_BRD2KO+Y113F-Y386F_2


title: TS576 cell, parental_2

description:
Library name: Sample 23
raw_counts_4.txt
TS576_2


title: GSC11 cells, BRD2_BD2_3

description:
Library name: Sample 18
raw_counts_1.txt
GSC11_BRD2KO+Y386F_3


title: GSC11 cells, shControl_1

description:
Library name: Sample 1
raw_counts_1.txt
GSC11_shCtrl_1

value: shControl


title: GSC11 cells, BRD2_BD1_3

description:
Library name: Sample 15
raw_counts_1.txt
GSC11_BRD2KO+Y113F_3


title: GSC11 cells, BRD2_BD2_1

description:
Library name: Sample 16
raw_counts_1.txt
GSC11_BRD2KO+Y386F_1


title: GSC11 cells, BRD2_BD1_1

description:
Library name: Sample 13
raw_counts_1.txt
GSC11_BRD2KO+Y113F_1


title: GSC11 cells, BRD2_WT_1

description:
Library name: Sample 10
raw_counts_1.txt
GSC11_BRD2KO+WT_1


title: GSC11 cells, RelA K310R_2

description:
Library name: Sample 8
raw_counts_1.txt
GSC11_K310R_2


title: GSC11 cells, shBRD2_2

description:
Library name: Sample 5
raw_counts_1.txt
GSC11_shBRD2_2


title: GSC11 cells, RelA K310R_1

description:
Library name: Sample 7
raw_counts_1.txt
GSC11_K310R_1


title: GSC11 cells, shBRD2_3

description:
Library name: Sample 6
raw_counts_1.txt
GSC11_shBRD2_3


title: pooled PBMC, 10x

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

description: Library name: PBMC_10x

data_processing:
In each tissue type, fastq files were subsetted to have an equal number of reads in data from each sample using seqtk. ScRNA-seq reads from 10x Genomics samples were mapped to human GRCh38 (GENCODE v32/Ensembl98) or mouse mm10 (GENCODE vM23/Ensembl98) reference genome using 10x Genomics Cell Ranger v9.0.1 software with default parameters. ScRNA-seq reads from SeekOne samples were mapped to human GRCh38 reference genome downloaded from seeksoultools v1.2.2 documentation site or mouse mm10 (GENCODE vM23/Ensembl98) reference genome built by Cell Ranger. Mapping was conducted using seeksoultools v1.2.2 with chemistry DDV2 and including introns. ScRNA-seq reads from MobiDrop samples were mapped to human GRCh38 (GENCODE v32/Ensembl98) or mouse mm10 (GENCODE vM23/Ensembl98) reference genome created by mobivision mkindex. Mapping was conducted using MobiVision v3.2 software. Count matrices were filtered using the R package pagoda2 v1.0.12. with minimal UMI count per cell was 1,000, maximal UMI count was 50,000, minimal number of genes per cell was 500 and minimal cells per gene number was 3. Doublets were identified using Scrublet v0.2.3. Decontamination was performed using DecontX from celda package v1.16.1. The following analysis was performed using the Seurat library. Seurat objects of PBMC samples were filtered with maximum percent of mitochondrial genes per cell set to 15%, maximum percent of hemoglobin genes per cell set to 2%, scrublet score lower than 0.2, number of total RNA count for each cell lower than 12,000, number of RNA features between 1,000 and 6,000. Cluster contaminated with neutrophil genes was removed. For murine adrenal samples and pancreatic neuroendocrine tumor samples cells having percent of mitochondrial genes more than 25%, percent of ribosomal genes more than 40%, scrublet score greater than 0.2, number of total RNA count greater than 50,000 and less than 500, number of RNA features lower than 250 were filtered out.
Assembly: GRCh38 (GENCODE v32/Ensembl98), mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
A patient's whole blood sample was diluted in PBS at a ratio of 1:1. Ficoll solution was added to a clean 15 ml falcon. The diluted blood sample was carefully layered on the Ficoll layer, preventing their mixing. Then, the sample was centrifuged with the following parameters: 450 g, 30 minutes, without brake. After that, the mononuclear cell ring was carefully collected from the Ficoll surface with a dispenser, and transferred to a clean 15 ml tube. The sample volume was brought to 10 ml using PBS. The sample was centrifuged at the parameters: 300 g for 10 minutes, after which the supernatant was removed. These steps were performed twice. Cryopreservation of the isolated cells was carried out according to the manufacturer's protocol. The samples were defrosted, washed, samples from 4 patients were pooled with 1 million cells from each patient for further loading onto the chip. Murine adrenal glands were excised and placed in PBS 1X with 10% fetal bovine serum (FBS) on ice. Under a binocular microscope, adipose tissue was removed with two tweezers/scalpel, and adrenal glands were mechanically homogenized with a scalpel on ice. Next, the adrenal gland homogenates were placed in a dissociating solution (HBSS buffer, Ca2+ 1.26 mM, collagenase IV 20 mg/mL, DNAse I 0.7 mg/ul, 0.5% BSA, RNase inhibitor) followed by 30-minute incubation at 37°C in a shaker-incubator (100 RPM). During the incubation, the suspension was pipetted every 10 minutes. Following the incubation, it was carefully pipetted, and 800 μl of PBS 1X with 10% FBS were added. The suspension was centrifuged 450 rcf for 6 min at +4◦C, then the supernatant was decanted, and the pellet was resuspended in 700 μl PBS 1X with 10% bovine serum and passed through a 70 μm filter. Then it was centrifuged 450 rcf 6 min at +4◦C, the supernatant was collected, the pellet was resuspended in 450 μl 1x PBS-0.05% BSA. The cell suspensions were gently mixed with cooled methanol in a ratio of 1:10 and placed for long-term storage at −80°C. For further work, the samples were defrosted on ice and rehydrated using a citrate buffer. Human pancreatic neuroendocrine tumor tissue was dissociated for single cell RNA sequencing using the Multi Tissue Dissociation Kit 2 by Miltenyi Biotec (cat. no. 130-110-203). Briefly, the tissue was placed in a petri dish on ice and cut into small pieces of 2–4 mm. The pieces were infused with the RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI/enzyme mix, attached to the sleeve of the single cell suspension dissociator (DSC-400) and run using the standard “H_Tumor_heater_1” program. After the termination of the program, the cells were centrifuged at 650 x g for 6 min at +4°C, resuspended in PBS 1X with 0.04 % bovine serum, passed through a 70 µm strainer and centrifugation was repeated. The supernatant was collected, the pellet was resuspended in 1 ml 1x PBS-0.04% BSA. Next, the cell suspension was fixed in cooled methanol. The cell suspension obtained in the previous step was mixed with methanol in a ratio of 1:10 and placed for long-term storage at −80°C. For further work, the samples were defrosted on ice and rehydrated using a citrate buffer.
The Chromium Next GEM Single Cell 5′ v2 Kit, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics, Pleasanton, CA, USA) and the Chromium Single Cell Controller Instrument were used to generate 10× single-cell libraries according to the manufacturer’s instructions. The SeekOne DD Single Cell 3’ Transcriptome-seq Kit v1.1 and the SeekOne Digital Droplet System Instrument were used to generate single-cell libraries according to the manufacturer’s instructions. The MobiCube Single-Cell 3’ RNA-seq Kit v2.0, MobiCube Single-Cell 5’ V(D)J Kit v1.0 and the MobiNovaSP-100 Instrument were used to generate single-cell libraries according to the manufacturer’s instructions.

value: PBMC

tag: disease status

value: type 1 diabetes mellitus


title: GSC11 cells, shControl_3

description:
Library name: Sample 3
raw_counts_1.txt
GSC11_shCtrl_3


title: GSC11 cells, shBRD2_1

description:
Library name: Sample 4
raw_counts_1.txt
GSC11_shBRD2_1


title: E4-Empty-Vector-Griptite-2

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description:
Library name: 23_HEK_Empty_Vector
Induction with doxycycline (0 ng/mL) was performed for 72 hours

data_processing:
Base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against hg38
The resulting BAM files were processed with FeatureCounts (Subreads) to yield count data for RefSeq transcript annotations
Transcripts Per Million (TPM) were calculated.
RefSeq annotations from NCBI Homo sapiens Annotation Release 110
Assembly: hg38
Supplementary files format and content: PS-18707_refseq_count.gct contains raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format
Supplementary files format and content: PS-18707_refseq_tpm.gct contains normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format

source_name: Embryonic kidney

extract_protocol:
HEK293 cells expressing inducible B3GALT2 or control (empty) vector or HEK293 wild-type cells were seeded at 500,000 cells per well in 12-well plates (Corning). HEK293 carrying inducible B3GALT2 and control-empty vector cells were incubated overnight and the next day incubated with 1000 ng/mL doxycycline (Sigma). All cell types were harvested 72 h after induction with doxycycline using the RNeasy® blood and tissue kit (QIAGEN) and RNA concentration was determined with NanoDrop™ Spectrophotometer (Thermo Scientific™).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB). Briefly, mRNAs were first enriched with oligo (dT) beads. Enriched mRNAs were fragmented for 15 min at 94°C. First strand and second strand cDNAs were subsequently synthesized. CDNA fragments were end repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated on the Agilent 5300 Fragment Analyzer (Agilent Technologies) and quantified by using Qubit 4.0 Fluorometer (Invitrogen). The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions.

value: Embryonic kidney

value: epithelial-like

value: inducible empty vector

value: empty vector overexpression


title: F4-Empty-Vector-Griptite-3

description:
Library name: 24_HEK_Empty_Vector
Induction with doxycycline (0 ng/mL) was performed for 72 hours


title: GSC11 cells, shControl_2

description:
Library name: Sample 2
raw_counts_1.txt
GSC11_shCtrl_2


title: C4-WT-Griptitite-3

description: Library name: 21_HEK_WT

value: wild type

value: untreated


title: B4-WT-Griptitite-2

description: Library name: 20_HEK_WT


title: PC3_input

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

description: Library name: PC3_input

data_processing:
Paired reads are aligned to UCSC hg38 genome using bwa with default parameters. Alignments that have MAPQ < 30 filtered out.
FASTQ files of replicates are merged.
After mates are fixed using samtools fixmate, alignments are sorted according to corrdinates. Duplicates are marked and removed using samtools markdup. Only properly paired alignments included in the next step.
NarrowPeaks are called with MACS3 callpeak with ' -BAMPE -g hs -q 0.00001 -B' parameters.
BedGraph files generated using bedtools genomecov with -bg as input of BAM files. The BedGraph files are converted to BigWig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeak

growth_protocol: PC3 cells were cultured in RPMI supplemented with 10% FBS for 48 hours. ~10 million cells per IP were double-crosslinked with 2 mM disuccinimidyl glutarate (DSG, Thermo Scientific Cat # 20593) for 45 minutes at room temperature followed by 1% formaldehyde (with approx. 10% methanol).

extract_protocol:
Crosslinked cells were lysed and sonicated as described previously (K. A. Holmes, G. D. Brown, J. S. Carroll, Methods Mol. Biol., 2016). Briefly, crosslinked cells were lysed and nuclei were enriched sequentially in Lysis buffer 1 (LB1: 50 mM HEPES—KOH, pH 7.5, 140 mM NaCl, 1 mM  EDTA, 10% glycerol, 0.5% Igepal CA-630, 0.25% Triton X-100), Lysis buffer 2 (LB2: 10 mM Tris—HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and Lysis  buffer 3 (LB3: 10 mM Tris—HCl,  pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine). Chromatin was fragmented using 4 minutes of active sonication (30 sec ON 60 sec OFF).
5 ng input and IP DNA was used for sequencing library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat # E7645, NEB) according to the manufacturer's instructions.Libraries were amplified using KAPA HiFi HotStart Ready Mix (Roche, Cat # KK2602) for 10 cycles. Amplified libraries were purified using Agencourt AMPure XP Beads (Beckman Coulter, Cat # A63881).

treatment_protocol: Untreated


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 4, scADT

city: Erlangen

first: Kilian

last: Schober

address: Wasserturmstraße 3/5

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Uniklinikum Erlangen/ Friedrich-Alexander-Universität Erlangen-Nürnberg

description:
Library name: Experiment2_Sample4_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV

data_processing:
scRNAseq
The sequencing sample was processed via the cellranger (version 7.1.0, 10x Genomics) `multi`-command.
Assembly: Gene expression reference: GRCh38 (version 2020A, 10x Genomics); VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics); and customized feature barcode references (see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV, Dextramer-barcodes.CSV
Supplementary files format and content: comma-separated value files and matrix files

extract_protocol:
PBMCs were thawed from cryopreserved stocks and rested overnight at 1x10^6 cells/mL in cRPMI medium (RPMI 1640 Medium + 10% heat-inactivated FCS, 0.05 mM β-mercaptoethanol, 0.05 mg/mL gentamicin, 1.1915 g/L HEPES, 0.2 g/L L-glutamine, 100 U/mL Penicillin-Streptomycin). For experiment 1+2: 5-10^6 PBMCs per donor and timepoint were recovered and first stained with a cocktail of differentially conjugated anti-CD45 surface antibodies and individual hashtag antibodies (2.5 µL per 5x10^6 PBMCs of TotalSeq-C anti-human hashtag antibodies 1–8, Biolegend, 394661, 394663, 394665, 394667, 394669, 394671, 394673, 394675) for 30 min on ice. Afterwards, up to 8 individual samples were pooled and were later distinguished by individual CD45 color-barcoding at the sorter and by individual TotalSeq-C anti-human hashtag antibodies in the scRNAseq dataset. During the incubation, a dextramer cocktail containing 13 different dextramers (experiment 1) or only the A2/NS4B214-dextramer (experiment 2). For this cocktail, 1 µL per 5x10^6 pooled cells of dCODE dextramers® (immudex) and 100 µM d-biotin (1/500 of total dextramer volume) were pre-mixed in FACS-buffer (PBS + 0.5% BSA) to block free binding sites. The pooled samples (40-60x10^6 cells) were stained with 400-600 µL of the dextramer cocktail for 30 min on ice. Then, 400-600 µL of a cocktail containing vaibility dye ZombieNir, fluorescently-labelled antibodies for cell sorting (anti-CD8, -CD4, -CD19, -CD56) and DNA-barcoded CITE-seq antibodies (BioLegend: anti-CD45RA (304163), -CD62L (304851), -CD95 (305651), -CCR7 (353251), -CXCR3 (353251))was added and cells were stained for additional 30 min on ice. Single, live, CD19-, CD56-, CD4-, CD8+, dextramer+ lymphocytes were sorted on a FACS Aria II cell sorter (BD) in previously FCS-coated 1.5 mL tubes filled with FACS-buffer. For experiment 3: 10x10^6 PBMCs per donor and timepoint were recovered and stained with pre-preapred dextramer cocktail (2µL A2/NS4B214-dextramer, 0.4µL 100µM d-Biotin in 100µL FACS-buffer) for 30 min on ice. dextramer+ cells were then enriched by magnetic cell separartion using the MACS Mini Separator (Miltenyi Biotec) with anti-PE microbeads following manufacturer's instructions. Enriched cells were then incubated with a mix of ZombieNir viability dye, fluorescently labeled surface antibodies (Anti-CD18, -CD56, -CD4, -CD8 and differentially-labelled anti-CD45 for donor-separation during sorting), donor -specific TotalSeq-C anti-human hashtag antibodies (as indicated for experiment 1+2) and CITEseq antibodies (as indicated above) for 30 min on ice. Up to 8 samples were then pooled into one sample for sorting and single, live, CD19-, CD56-, CD4-, CD8+, dextramer+ lymphocytes were sorted on a FACS Aria II cell sorter (BD) in previously FCS-coated 1.5 mL tubes filled with FACS-buffer. For all experiments: Immediately after sorting, cells were loaded to a Chromium Next GEM Chip K (10X Genomics) and Chromium Next GEM Single-Cell 5′ kits v.2 were used to generate GEX, VDJ and CITEseq libraries according to the manufacturer’s instructions (10X Genomics, 1000263, 1000256, 1000252, 1000286, 1000250, 1000215, 1000190). Libraries were sent to Novogene and sequenced on an Illumina NovaSeq platform with PE150 strategy.
Library construction for scRNAseq was performed according to manufacturer's instructions (10x Genomics) for 5' GEX, VDJ and CITEseq, V2 chemistry dual index.

value: T cells

value: Yellow Fever vaccination

tag: batch

value: Experiment 2


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 3, scADT

description:
Library name: Experiment2_Sample3_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 1, scADT

description:
Library name: Experiment2_Sample1_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 4, scADT

description:
Library name: Experiment1_Sample4_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV

value: Experiment 1


title: A4-WT-Griptitite-1

description: Library name: 19_HEK_WT


title: F3-B3GALT2-Griptite-3

description:
Library name: 18_HEK_B3GALT2
Induction with doxycycline (0 ng/mL) was performed for 72 hours

value: inducible vector for B3GALT2 overexpression

value: B3GALT2 overexpression


title: D3-B3GALT2-Griptite-1

description:
Library name: 16_HEK_B3GALT2
Induction with doxycycline (0 ng/mL) was performed for 72 hours


title: pooled PBMC, SeekOne

description: Library name: PBMC_SeekOne


title: PC3_SMARCD2

description: Library name: PC3_SMARCD2


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 3, Sample 1, scADT

description:
Library name: Experiment3_Sample1_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV

value: Experiment 3


title: D4-Empty-Vector-Griptite-1

description:
Library name: 22_HEK_Empty_Vector
Induction with doxycycline (0 ng/mL) was performed for 72 hours


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 2, scADT

description:
Library name: Experiment2_Sample2_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 3, scADT

description:
Library name: Experiment1_Sample3_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 2, scADT

description:
Library name: Experiment1_Sample2_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 1, scADT

description:
Library name: Experiment1_Sample1_ADT
10x Genomics, see Hashtag-barcodes.CSV, CITEseq-barcodes.CSV Dextramer-barcodes.CSV, Sample_annotations.CSV


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 3, Sample 1, scVDJ

description:
Library name: Experiment3_Sample1_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 1, scVDJ

description:
Library name: Experiment2_Sample1_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 4, scVDJ

description:
Library name: Experiment1_Sample4_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 2, scVDJ

description:
Library name: Experiment1_Sample2_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 4, scVDJ

description:
Library name: Experiment2_Sample4_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 3, scVDJ

description:
Library name: Experiment2_Sample3_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 3, scGEX

description:
Library name: Experiment2_Sample3_GEX
10x Genomics


title: E3-B3GALT2-Griptite-2

description:
Library name: 17_HEK_B3GALT2
Induction with doxycycline (0 ng/mL) was performed for 72 hours


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 1, scGEX

description:
Library name: Experiment2_Sample1_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 2, scVDJ

description:
Library name: Experiment2_Sample2_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 3, scVDJ

description:
Library name: Experiment1_Sample3_VDJ
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 3, Sample 1, scGEX

description:
Library name: Experiment3_Sample1_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 4, scGEX

description:
Library name: Experiment2_Sample4_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 1, scGEX

description:
Library name: Experiment1_Sample1_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 4, scGEX

description:
Library name: Experiment1_Sample4_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 3, scGEX

description:
Library name: Experiment1_Sample3_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 2, scGEX

description:
Library name: Experiment1_Sample2_GEX
10x Genomics


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 1, Sample 1, scVDJ

description:
Library name: Experiment1_Sample1_VDJ
10x Genomics


city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

description: Library name: SI_34245_EPN1425_Citraconate_24h_H3K4me3

data_processing:
aligned to hg38 using bwa mem
filtered alignments using samtools and picard
macs peak calling
Assembly: mm10, hg38
Supplementary files format and content: bigwigs (.bw)
Supplementary files format and content: bed peak files (.bed)

source_name: Brain Tumor

growth_protocol: EPN-1425 cells  were cultured in DMEM media (Gibco #11965092) supplemented with 10% fetal bovine serum (VWR #89510-186) and L-glutamine, 200mM (Thermo Fisher Scientific #A2916801). ZFTA-RELA mNSCs were cultured in Neurobasal media (Gibco #21103049) with 0.2 % heparin solution (StemCell Technologies Inc. #07980), 20ng/μL EGF (Shenandoah #100-26) and 20ng/μL FGF-Basic 154aa (Shenandoah #100-146).

extract_protocol:
1 million cells were used per ChIP reaction with 2ug of antibody. Briefly, cells were crosslinked for 10 minutes in a 1% formaldehyde solution, followed by quenching with 1/10th the volume of 1.25M glycine for 5 minutes at room temperature. Following this, the cells were lysed and sonicated (Bioruptor Pico, Diagenode) to a desired chromatin size of about 200bp using the Easy mode cycle.
About 1-10ng of ChIP DNA were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase [New England BioLabs (NEB)]. Klenow fragment (3′ to 5′ exo minus; NEB) was used to add a single adenine base to fragment ends, followed by ligation of Illumina adaptors (Quick ligase, NEB). PCR enriched the adaptor-ligated DNA fragments using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza), followed by gel extraction using QIAEX II reagents (Qiagen). Quantified libraries quality-checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: EPN1425 and ZFTA-RELA mNSCs were treated with DMSO/10mM Citraconate for 24h/48h or 10µM GSK343 for 96h

value: Brain Tumor

value: Tumor

value: Citraconate 10mM

tag: antibody

value: H3K4me3 Chip Antibody:CST, # 9751S


title: SI_39409_EPN1425_DMSO_H3K27me3_R1

description: Library name: SI_39409_EPN1425_DMSO_H3K27me3_R1

value: DMSO

value: H3K27me3 Chip Antibody:Millipore, # 07-449


title: SI_39410_EPN1425_DMSO_H3K27me3

description: Library name: SI_39410_EPN1425_DMSO_H3K27me3


title: Pooled CD8 T cells, post yellow fever virus vaccination, Experiment 2, Sample 2, scGEX

description:
Library name: Experiment2_Sample2_GEX
10x Genomics

value: PBMC


title: SI_34243_EPN1425_DMSO_H3K4me3

description: Library name: SI_34243_EPN1425_DMSO_H3K4me3


description: Library name: SI_39412_EPN1425_10mM_Citraconate_H3K27me3


description: Library name: SI_39407_EPN1425_10mM_Citraconate_H3K4me3


title: SI_39405_EPN1425_DMSO_H3K4me3

description: Library name: SI_39405_EPN1425_DMSO_H3K4me3


description: Library name: SI_39411_EPN1425_10mM_Citraconate_H3K27me3


title: SI_39406_EPN1425_DMSO_H3K4me3

description: Library name: SI_39406_EPN1425_DMSO_H3K4me3


description: Library name: SI_39408_EPN1425_10mM_Citraconate_H3K4me3


title: U2OS cells, C19MC, control-2

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: OBGYN

institute: University of Pittsburgh

description: Library name: JFMU11

data_processing:
Fastq files were aligned to human genome using software STAR (v2.7.0), with GENCODE v30 annotation.
Reads per gene were summarized using STAR.
R pakcage DESeq2 was usied to normalized data and identify differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: csv file, with reads per gene for each sample.

growth_protocol: BeWo cells were maintained in F12K supplemented with 10% GemCell SuperCalf serum, and antibiotics.  U2OS cells were cultured in DMEM supplemented with 10% GemCell SuperCalf serum and antibiotics. Cells were maintained in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Total RNA samples were prepared using TRI reagent and purified using EconoSpin columns (Epoch Life Science). An on-column Dnase step, using RNase-free Dnase (Qiagen) was included.
RNA libraries were prepared and sequenced at Novogene.

treatment_protocol: When indicated cells were exposed to poly(I:C) at 10 ug/ml overnight.

value: Osteosarcoma

value: transfected BAC-C19MC

value: Control


title: U2OS cells, WT, poly(I:C)-2

description: Library name: JFMU10

value: WT


title: U2OS cells, C19MC, poly(I:C)-2

description: Library name: JFMU12


title: U2OS cells, C19MC, control-1

description: Library name: JFMU7


title: U2OS cells, WT, poly(I:C)-1

description: Library name: JFMU6


title: BeWo cells dA11, poly(I:C)-3

description: Library name: JFMB8

source_name: BeWo

value: BeWo

value: Choriocarcinoma

value: ATAC-11 KO


title: BeWo cells dA11, poly(I:C)-2

description: Library name: JFMB4


title: BeWo cells dA11, control-3

description: Library name: JFMB7


title: BeWo cells dA11, control-2

description: Library name: JFMB2


title: BeWo cells WT, poly(I:C)-2

description: Library name: JFMB3


title: BeWo cells WT, control-2

description: Library name: JFMB1


title: BeWo cells WT, control-3

description: Library name: JFMB5


title: BeWo cells WT, poly(I:C)-1

description: Library name: JF2


title: BeWo cells WT, control-1

description: Library name: JF1


title: PARP1, EGFR-AS1-OE, 50μM etoposide, rep2

city: Nanjing

first: Changying

last: Guo

state: Jiangsu

address: Longmian Avenue, No. 639

department: School of Life Science and Technology

institute: China Pharmaceutical university

description: Library name: PARP1-AS1-OE-Etop-rep2

data_processing:
Rawdata were filter by Fastp (v0.12.4) to remove low quality reads and adaptor sequence. The parameters for fastp are listed as follows: "-g -q 5 -u 50 -n 15 -l 150"
High quality and adaptor-removed clean data were submitted to Bowtie2 (v2.25) for alignment using hg19 assembly. The parameters for bowtie2 are: "  --reorder   --very-sensitive-local -x hg19 --local --no-mixed --no-discordant  --phred33 -I 10 -X 700"
Mapped reads contain abundant redundant duplicates were tagged by Picard tools (v2.27.1) .
To obtain enriched peaks over the local background, MACS2 software (v2.2.6) was used with arguments “-f BEMPE -q 0.01” for narrow peak. In addition, “--min-length” parameter also configurated depend on average length of peaks.
To obtain portable coverage plots, bam file ere converted to bigwig file using deeptools (v3.5.1) with arguments "-normalizeUsing RPGC --binSize 20 --effectiveGenomeSize 2864785220 -p max --smoothLength 40  --ignoreDuplicates   --extendReads".
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: RPMI-1640, 10% fetal bovine serum. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were treated with Con-A beads, antibodies and reagents following the instrunction of Hyperactive In-Situ ChIP Library Prep Kit.
Libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina from Vazyme biotech co.. Two hundred thousand cells were used as starting material for samples. Library were amplified using appropriate cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using VAHTS DNA Clean Beads from Vazyme biotech co.. Libraries were validated using Qubit, AATI and QPCR.

treatment_protocol: vehicle or 50μM etoposide, 30min

value: cell line

value: 50μM etoposide, 30min

value: Santa Cruz, sc-8007


title: PARP1, EGFR-AS1-OE, Vehicle, rep2

description: Library name: PARP1-AS1-OE-Vehicle-rep2

value: Vehicle, 30min


title: BeWo cells dA11, poly(I:C)-1

description: Library name: JF6


title: BeWo cells dA11, control-1

description: Library name: JF5


title: PARP1, EGFR-AS1-OE, Vehicle, rep1

description: Library name: PARP1-AS1-OE-Vehicle-rep1


title: U2OS cells, C19MC, poly(I:C)-1

description: Library name: JFMU8


title: U2OS cells, WT, control-2

description: Library name: JFMU9


title: PARP1, vector, Vehicle, rep2

description: Library name: PARP1-Vec-Vehicle-rep2

value: vector-control


title: PARP1, vector, 50μM etoposide, rep2

description: Library name: PARP1-Vec-Etop-rep2


title: PARP1, EGFR-AS1-OE, 50μM etoposide, rep1

description: Library name: PARP1-AS1-OE-Etop-rep1


title: PARP1, vector, Vehicle, rep1

description: Library name: PARP1-Vec-Vehicle-rep1


title: PARP1, vector, 50μM etoposide, rep1

description: Library name: PARP1-Vec-Etop-rep1


title: U2OS cells, WT, control-1

description: Library name: JFMU5


title: HEK293T cell, VEGFA, A3C, loop2-22-25-5-M, PE2, rep1

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

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

department: School of Life Sciences

institute: Westlake university

description:
609218
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1

growth_protocol: The culture conditions for HEK293T cells typically involve maintaining the cells in a high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin antibiotic solution. The medium is further enriched with 2 mM L-glutamine for optimal cell growth and health. Cells should be cultured at 37°C in a humidified atmosphere with 5% CO2. Regular media replacement is essential, usually every 2-3 days, to prevent the accumulation of metabolic waste and to supply fresh nutrients. When the cell confluence reaches about 80-90%, subculturing is recommended to avoid overgrowth, commonly achieved by detaching the cells using trypsin and splitting them into fresh culture flasks at a suitable dilution ratio, typically around 1:10.

extract_protocol:
Genomic DNA was extracted by the addition of 20 µl of freshly prepared lysis buffer (10 mM Tris-HCl, pH 7.5; 0.05% SDS (ThermoFisher Scientific); 25 µg/ml proteinase K (Tiangen)) directly into each tube which 30,000 cells were sorted from each sample. The genomic DNA mixture was incubated at 37 °C for 1.5 h, followed by an 80 °C enzyme inactivation step for 30 min.
Use site-specific primers with second-generation sequencing adapters to amplify target sites via PCR for library construction.

treatment_protocol: HEK293T cells were seeded on 12-well poly-d-lysine coated plates (Corning). Between 16 and 24 h after seeding, cells were transfected at approximately 70% confluency with lipofectamine 3000 (ThermoFisher Scientific) according to the manufacturer’s protocols and 3249 ng All in one(PE2) plasmid, and 1083 ng sgRNA plasmid (for PE2 and PE3). Unless otherwise stated, cells were cultured for 2 days following transfection, after which the medium was removed, the cells were washed with 1 ml 1×PBS (ThermoFisher Scientific), then digested with 0.25% Trypsin-EDTA (1X) (Gibco) for 1 min, 1 ml DMEM complete medium was added to terminate the reaction. Centrifugation at 300 g for 5 min, discard supernatant and resuspended with 150 ul 1×PBS (ThermoFisher Scientific). After resuspended, all positive cells (single or double fluorescence positive) were sorted and collected into a 1.5 ml low adsorption centrifuge tube (ThermoFisher Scientific) by MULTI-APPLICATION CELL SORTER MA900 (Sony). Centrifugation at 11,200 g for 1 min, discard supernatant and store at -20°C for a long time.

value: base editing by prime editing


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-31-7-M, PE2, rep3

description:
5929r
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-22-25-5-M, PE2, rep3

description:
609418
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-51-5-M, PE2, rep2

description:
70353
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-51-5-M, PE2, rep1

description:
70352
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-22-25-5-M, PE2, rep2

description:
609318
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-51-5-M, PE2, rep3

description:
70354
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, loop2-27-51-5-M, PE2, rep1

description:
70342
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, loop2-27-51-5-M, PE2, rep3

description:
70344
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, epegRNA+loop2-26-43-5-M, PE2, rep3

description:
70284
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, epegRNA+loop2-26-43-5-M, PE2, rep2

description:
70283
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-31-7-M, PE2, rep2

description:
5765r
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, loop2-23-31-7-M, PE2, rep2

description:
5764r
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, epegRNA+loop2-26-43-5-M, PE2, rep1

description:
70282
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, loop2-26-43-5-M, PE2, rep2

description:
70272
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, loop2-26-43-5-M, PE2, rep1

description:
70271
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, epegRNA, PE2, rep3

description:
70264
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, epegRNA, PE2, rep1

description:
70261
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, epegRNA+loop2-28-43-5-M, PE2, rep3

description:
70254
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, epegRNA+loop2-28-43-5-M, PE2, rep2

description:
70253
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, epegRNA+loop2-28-43-5-M, PE2, rep1

description:
70252
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, loop2-28-43-5-M, PE2, rep3

description:
70244
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, loop2-28-43-5-M, PE2, rep1

description:
70242
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, loop2-27-51-5-M, PE2, rep2

description:
70343
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, loop2-28-43-5-M, PE2, rep2

description:
70243
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +4Cins, epegRNA, PE2, rep3

description:
70234
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: BeWo cells WT, poly(I:C)-3

description: Library name: JFMB6


title: HEK293T cell, DNMT1, +4Cins, epegRNA, PE2, rep1

description:
70232
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, loop2-23-37-5-M, PE2, rep3

description:
70214
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, loop2-26-43-5-M, PE2, rep3

description:
70274
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, epegRNA+loop2-23-37-5-M, PE2, rep3

description:
70194
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, epegRNA, PE2, rep3

description:
70204
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, epegRNA+loop2-23-37-5-M, PE2, rep3

description:
70223
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, epegRNA, PE2, rep2

description:
70202
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, epegRNA+loop2-23-37-5-M, PE2, rep1

description:
70221
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, epegRNA+loop2-23-37-5-M, PE2, rep2

description:
70193
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, loop2-23-37-5-M, PE2, rep2

description:
70213
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, epegRNA+loop2-23-37-5-M, PE2, rep2

description:
70222
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, loop2-23-37-5-M, PE2, rep1

description:
70211
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, epegRNA, PE2, rep3

description:
70174
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, loop2-23-37-5-M, PE2, rep2

description:
70182
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, epegRNA, PE2, rep2

description:
70173
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, loop2-23-37-5-M, PE2, rep1

description:
70181
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, G4A, epegRNA, PE2, rep1

description:
70201
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, epegRNA+loop2-28-50-5-M, PE2, rep1

description:
70121
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, epegRNA+loop2-28-50-5-M, PE2, rep3

description:
70123
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, loop2-23-37-5-M, PE2, rep3

description:
70184
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, epegRNA, PE2, rep2

description:
70102
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, epegRNA, PE2, rep1

description:
70171
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, +3Adel, epegRNA, PE2, rep2

description:
70262
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, loop2-28-50-5-M, PE2, rep3

description:
70113
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2G, epegRNA+loop2-23-37-5-M, PE2, rep1

description:
70192
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, epegRNA+loop2-28-50-5-M, PE2, rep2

description:
70122
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, loop2-28-50-5-M, PE2, rep2

description:
70112
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, epegRNA, PE2, rep3

description:
70104
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, loop2-28-50-5-M, PE2, rep1

description:
70111
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, epegRNA+loop2-28-50-5-M, PE2, rep3

description:
70093
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, epegRNA+loop2-28-50-5-M, PE2, rep1

description:
70091
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, epegRNA+loop2-28-50-5-M, PE2, rep2

description:
70092
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G4C, epegRNA, PE2, rep1

description:
70101
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, loop2-28-50-5-M, PE2, rep3

description:
70083
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, loop2-28-50-5-M, PE2, rep2

description:
70082
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, loop2-28-50-5-M, PE2, rep1

description:
70081
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A2C, loop2-28-50-5-M, PE2, rep3

description:
70053
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, epegRNA, PE2, rep1

description:
70071
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, A3G, epegRNA, PE2, rep2

description:
70073
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1