title: Control EcSCs 3

city: Shanghai

first: Yuqi

last: Yang

address: No. 826 Zhangheng Road, Pudong New District, Shanghai

department: Department of Pharmacology

institute: School of Pharmacy, Fudan University

description: Library name: Sample12

data_processing:
Quality Control: The raw sequencing data were processed using Cutadapt (v1.9.1) to remove technical sequences, including adapters and PCR primers, and to filter out bases with a quality score lower than 20. The parameters set included a Phred cutoff of 20, an error rate of 0.1, adapter overlap of 1 bp, a minimum length of 75, and a proportion of N set to 0.1 to generate high-quality clean data.
Read Alignment: Clean data were aligned to the reference genome using Hisat2 (v2.0.1). First, reference genome sequences and gene model annotation files of the relevant species were downloaded from genomic databases such as UCSC, NCBI, and ENSEMBL. Hisat2 was then used to index the reference genome sequence.
Expression Analysis: For expression quantification, transcripts in FASTA format were generated from known GFF annotation files, and the expression levels of genes and isoforms were estimated using HTSeq (v0.6.1) with the clean data as input.
Differential Expression Analysis: The DESeq2 package from Bioconductor was used to analyze differential expression, applying a model based on the negative binomial distribution, with adjustments for multiple testing. Genes were considered differentially expressed if their adjusted p-values (Padj) were less than 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing FPKM values for  all samples 1&4 combined, with columns for gene ID, gene length, sample counts, FPKM values, chromosome info, and gene annotations.
Supplementary files format and content: Tab-delimited text file containing FPKM values for  all samples 2&3&5&6 combined, with columns for gene ID, gene length, sample counts, FPKM values, chromosome info, and gene annotations.
Supplementary files format and content: Tab-delimited text file containing FPKM values for  all samples 7-12 combined, with columns for gene ID, gene length, sample counts, FPKM values, chromosome info, and gene annotations.

source_name: Endometriosis tissue

growth_protocol: The cells were cultured in DMEM-F12 complete medium containing 10% fetal bovine serum and incubated at 37°C in a 5% CO2 environment. The medium was replaced every 2 to 3 days. Cells were passaged after about one week of confluence.

extract_protocol:
RNA extraction was performed using the FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme, China) according to the manufacturer’s guidelines.
RNA libraries were prepared foe sequencing using standard Illumina protocols.

treatment_protocol: Lentiviral particles expressing sgRNA (targeting HOXC4) and Cas9 protein were harvested to infect human primary endometrial and endometriotic stromal cells, with 2 μg/ml Polybrene added to improve infection efficiency. The cells were subsequently cultured in complete media containing 2 μg/ml puromycin for 7 days. The gene knockout efficiency of the selected cells was confirmed using Western blot analysis.

value: Endometriosis tissue

value: Primary endometriotic stromal cells

value: Human Endometriotic Stromal Cells


title: PBMC_IgG+ B cells, CD4 = 10 cells/ul

status: Public on Sep 30 2025

type: SRA

city: Hefei

first: Lina

last: Huang

state: 安徽

address: Hefei in Anhui Province

country: China

institute: university of science and technology in China

description: Library name: 4#

library_source: transcriptomic

data_processing:
Sequencing was performed on the Illumina Novaseq 6000 platform, yielding 10M of PE150 reads for the BCR library and 5M of PE150 reads for the TCR library. Data processing of raw reads was quality checked by using fastqc v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed for low-quality bases and adaptors, if necessary, by using TrimGalore
MiGEC software was used to identify primers for each gene in the sequences, followed by demultiplexing of the quality-filtered sequences based on their primer sequences
MiGEC software was used to analyze the CDR3 sequences and identity VDJ segment positions for each gene
Assembly: hg38
Supplementary files format and content: xlsx files about BCR and TCR repertoires and Frequency
Library strategy: BCR-Seq

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Total RNA was extracted using TRIzol reagents and quantified by Qubit. RNA integrity was measured using Agilent 2100 bioanalyzer and only samples with RIN higher than 7 were used for library preparation.
For PBMC samples, typically 100 ng of total RNA was used as a template. cDNA synthesis was performed according to smart-seq2 protocol with some modifications

tag: tissue

value: PBMC

tag: cell line

value: Lymphocyte

tag: cell type

value: B cell


title: PBMC_IgG+ B cells, CD4 = 11 cells/ul

description: Library name: 3#


title: Control EcSCs 1

description: Library name: Sample10


title: HOXC4 KO EcSCs 3

description: Library name: Sample9

tag: treatment

value: HOXC4 knockout


title: Control EcSCs 2

description: Library name: Sample11


title: PBMC_IgG+ B cells, CD4 = 29 cells/ul

description: Library name: 2#


title: EcSCs 3

description: Library name: Sample3


title: ESCs 2

description: Library name: Sample5

source_name: Eutopic endometrium

value: Eutopic endometrium

value: Primary endometrial stromal cells

value: Human Endometrial Stromal Cells


title: ESCs 1

description: Library name: Sample4


title: EcSCs 2

description: Library name: Sample2


title: ESCs 3

description: Library name: Sample6


title: STR_RUN5_HTO

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: STR_RUN5_HTO

library_source: other

data_processing:
10x Cellranger pipeline was used to process raw fastq files, using feature barcoding
Assembly: hg38
Supplementary files format and content: raw counts matrixes from Cellranger pipeline output

molecule: protein

source_name: Small Intestine

extract_protocol:
Cells from surgical intestinal tissue were defrosted. Tissue was processed to yield high viability single cells, enriched for Epithelial/Stromal/Immune fractions and then cells were tagged with CITE-seq and hashing antibodies. Stromal cells were further subjected to LeviCell enrichment for high quality cells. Cells were pooled and loaded on to the 10X platform for single-cell RNA sequencing.
Pooled tagged samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX), Antibody tagged oligo (ADT - with CITE-seq proteins and hashing information and T-cell receptor (TCR) library amplification and indexing, as per protocol CG000186 (Rev A).
RNA-Seq paired-end

value: Small Intestine

tag: chemistry

value: 5' Chemistry, 10x

tag: cell isolation

value: CD45- EPCAM-

tag: library type

value: Feature Barcoding

tag: multiplexed sample

value: HTO4:Stric.Inv,TIP 652,HTO1:Inf.Inv,TIP 420,HTO3:Stric.Inv,GI 7833,HTO2:HC,TIP 525,HTO1:Inf.Inv,TIP 420,HTO3:Stric.Inv,GI 7833,HTO2:HC,TIP 525,HTO4:Stric.Inv,TIP 652

tag: disease

value: Crohn's Disease


title: STR_RUN4_HTO

description: Library name: STR_RUN4_HTO

value: HTO4:Stric.N.Inv,GI 7738, HTO3:Stric.Inv,GI 7738, HTO2:Fist.Inv,TIP 535,HTO1:Fist.Inv,GI 6239


title: EcSCs 1

description: Library name: Sample1

value: Endometriosis tissue


title: STR_RUN4_GEX

description: Library name: STR_RUN4_GEX

library_source: transcriptomic single cell

molecule: polyA RNA

value: Gene Expression


title: STR_RUN3_HTO

description: Library name: STR_RUN3_HTO

value: HTO4:Inf.N.Inv,TIP 651, HTO6:Stric.N.Inv,IBD 38,HTO1:Fist.Inv,TIP 559,HTO7:HC,TIP 633,HTO5:Stric.Inv,IBD 38,HTO2:Fist.N.Inv,TIP 559,HTO3:Inf.Inv,TIP 651


title: STR_RUN3_GEX

description: Library name: STR_RUN3_GEX


title: STR_RUN2_HTO

description: Library name: STR_RUN2_HTO

value: HTO5:Stric.Inv, GI 7595, HTO3:Inf.Inv, GI 7071,HTO1:Fist.Inv, TIP 535, HTO7:HC, GI 6968, HTO6:Stric.N.Inv, GI 7595, HTO4:Inf.N.Inv, GI 7071, HTO2:Fist.N.Inv,TIP 535


title: STR_RUN1_HTO

description: Library name: STR_RUN1_HTO

value: HTO4:Inf.N.Inv, GI 6788, HTO2:Fist.N.Inv, TIP 473, HTO1:Fist.Inv, TIP 473, HTO5:HC, TIP 522, HTO3:Inf.Inv, GI6788


title: STR_RUN1_GEX

description: Library name: STR_RUN1_GEX


title: HOXC4 KO EcSCs 2

description: Library name: Sample8

value: Primary endometriotic stromal cells

value: Human Endometriotic Stromal Cells


title: HOXC4 KO EcSCs 1

description: Library name: Sample7

value: HOXC4 knockout


title: CD45_RUN5_HTO

description: Library name: CD45_RUN5_HTO


title: CD45_RUN5_GEX

description: Library name: CD45_RUN5_GEX


title: CD45_RUN4_HTO

description: Library name: CD45_RUN4_HTO


title: CD45_RUN4_GEX

description: Library name: CD45_RUN4_GEX


title: STR_RUN5_GEX

description: Library name: STR_RUN5_GEX


title: CD45_RUN3_TCR

description: Library name: CD45_RUN3_TCR

value: VDJ Profiling


title: CD45_RUN2_HTO

description: Library name: CD45_RUN2_HTO


title: CD45_RUN1_HTO

description: Library name: CD45_RUN1_HTO


title: CD45_RUN1_TCR

description: Library name: CD45_RUN1_TCR


title: CD45_RUN1_GEX

description: Library name: CD45_RUN1_GEX


title: CD45_RUN3_GEX

description: Library name: CD45_RUN3_GEX


title: CD45_RUN5_TCR

description: Library name: CD45_RUN5_TCR


title: EPI2_RUN5_TCR

description: Library name: EPI2_RUN5_TCR

value: EPCAM+


title: EPI2_RUN5_HTO

description: Library name: EPI2_RUN5_HTO

value: Small Intestine


title: EPI1_RUN5_HTO

description: Library name: EPI1_RUN5_HTO

value: 5' Chemistry, 10x


title: CD45_RUN4_TCR

description: Library name: CD45_RUN4_TCR


title: EPI1_RUN5_GEX

description: Library name: EPI1_RUN5_GEX


title: CD45_RUN3_HTO

description: Library name: CD45_RUN3_HTO


title: STR_RUN2_GEX

description: Library name: STR_RUN2_GEX

value: CD45- EPCAM-


title: EPI2_RUN4_HTO

description: Library name: EPI2_RUN4_HTO

value: Feature Barcoding


title: EPI2_RUN5_GEX

description: Library name: EPI2_RUN5_GEX

value: HTO4:Stric.Inv,TIP 652,HTO1:Inf.Inv,TIP 420,HTO3:Stric.Inv,GI 7833,HTO2:HC,TIP 525,HTO1:Inf.Inv,TIP 420,HTO3:Stric.Inv,GI 7833,HTO2:HC,TIP 525,HTO4:Stric.Inv,TIP 652


title: CD45_RUN2_GEX

description: Library name: CD45_RUN2_GEX

value: Crohn's Disease


title: EPI1_RUN4_HTO

description: Library name: EPI1_RUN4_HTO

value: HTO4:Stric.N.Inv,GI 7738, HTO3:Stric.Inv,GI 7738, HTO2:Fist.Inv,TIP 535,HTO1:Fist.Inv,GI 6239


title: EPI1_RUN4_GEX

description: Library name: EPI1_RUN4_GEX


title: CD45_RUN2_TCR

description: Library name: CD45_RUN2_TCR


title: EPI2_RUN3_TCR

description: Library name: EPI2_RUN3_TCR


title: EPI2_RUN3_HTO

description: Library name: EPI2_RUN3_HTO


title: EPI1_RUN3_HTO

description: Library name: EPI1_RUN3_HTO


title: EPI1_RUN3_GEX

description: Library name: EPI1_RUN3_GEX


title: EPI2_RUN2_TCR

description: Library name: EPI2_RUN2_TCR


title: EPI1_RUN5_TCR

description: Library name: EPI1_RUN5_TCR


title: EPI1_RUN2_GEX

description: Library name: EPI1_RUN2_GEX


title: EPI1_RUN1_GEX

description: Library name: EPI1_RUN1_GEX


title: STR5_Levicell_HTO

description: Library name: STR5_Levicell_HTO

value: HTO1:Fist. Inv, TIP 535 ECF, HTO2:Fist. Inv, TIP 535 FIST TRACT, HTO3:Fist.Inv, TIP 559, HTO4:Strict. Inv, GI 6966


title: STR3_Levicell_HTO

description: Library name: STR3_Levicell_HTO

value: HTO6:Inf.Inv, TIP 651, HTO2:IBD 38, Strict.Inv, HTO3:Healthy, TIP 852, HTO4:Healthy, GI 8366


title: STR4_Levicell_GEX

description: Library name: STR4_Levicell_GEX

value: Gene Expression


title: STR6_Levicell_GEX

description: Library name: STR6_Levicell_GEX


title: STR5_Levicell_GEX

description: Library name: STR5_Levicell_GEX


title: STR6_Levicell_HTO

description: Library name: STR6_Levicell_HTO


title: EPI2_RUN4_TCR

description: Library name: EPI2_RUN4_TCR


title: STR1_Levicell_HTO

description: Library name: STR1_Levicell_HTO

value: HTO7:Fist.Inv, TIP535, HTO2:Fist.Inv, GI 6239, HTO3:Inf. Inv, TIP 815, HTO2:Inf.Inv, GI 7812


title: EPI2_RUN4_GEX

description: Library name: EPI2_RUN4_GEX


title: STR2_Levicell_GEX

description: Library name: STR2_Levicell_GEX


title: STR1_Levicell_GEX

description: Library name: STR1_Levicell_GEX


title: EPI2_RUN2_HTO

description: Library name: EPI2_RUN2_HTO

value: HTO5:Stric.Inv, GI 7595, HTO3:Inf.Inv, GI 7071,HTO1:Fist.Inv, TIP 535, HTO7:HC, GI 6968, HTO6:Stric.N.Inv, GI 7595, HTO4:Inf.N.Inv, GI 7071, HTO2:Fist.N.Inv,TIP 535


title: EPI2_RUN3_GEX

description: Library name: EPI2_RUN3_GEX

value: HTO4:Inf.N.Inv,TIP 651, HTO6:Stric.N.Inv,IBD 38,HTO1:Fist.Inv,TIP 559,HTO7:HC,TIP 633,HTO5:Stric.Inv,IBD 38,HTO2:Fist.N.Inv,TIP 559,HTO3:Inf.Inv,TIP 651


title: iCtrl Hc+GE D084

city: Los Angeles

first: Ranmal

middle: Aloka

last: Samarasinghe

state: California

address: 710 Westwood Plaza

department: Neurology

country: USA

institute: University of California, Los Angeles

data_processing:
The FASTQ file sequencing data for each assembloid condition (iCtrl Cx+GE day 120, Mut P1 Cx+GE day 120, iCtrl Hc+GE day 120, Mut P1 Hc+GE day 120, iCtrl Hc+GE day 84, Mut P1 Hc+GE day 84) were processed using the Cell Ranger 7.1.0 pipeline to generate count data which is provided as processed data files. These were subsequently analyzed using custom Python v3.11.8 based scripts that implemented the Scanpy v1.9.8 single cell analysis package as described in the associated manuscript.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered feature bc matrix containing the following files: barcodes.tsv, features.tsv, matrix.mtx

molecule: nuclear RNA

source_name: brain assembloid

growth_protocol: isogenic SCN8A patient IPSC (WT control and SCN8A mutant) were maintained under mouse embryonic fibroblast-supported conditions using DMEM/F12 (HyClone) with 20% knockout serum replacement (KSR, Invitrogen) and media supplements as described in Watanabe et al Cell Reprorts 2017 (https://doi.org/10.1016/j.celrep.2017.09.047)

extract_protocol:
3-11 assembloids per condition (across all batches) underwent the dissociation/sample preparation steps. All sample preparation steps were performed on dry ice or ice to minimize degradation effects from sample thawing or humidity. Tissue chunks were transferred to pre-cooled Dounce tissue grinder (Millipore Sigma, D9063), and homogenized in RNase-free conditions with a light detergent (0.001% Triton 100X/1% BSA/RNase Inhibitor (0.2U/µL)/0.5X Protease Inhibitor/1µM DTT/PBS). The homogenate was filtered through a 40 µm micro-cell strainer (Diagnocine, FNK-HT-AMS-04002) to remove large material and centrifuged at 1000g for 8 min at 4ºC to pellet away from debris. The nuclei pellet was washed two more times with PBS/1% BSA/RNase Inhibitor and spun down at 500g for 5 mins. The pellet was then suspended in wash buffer for quality assessment and concentration measurement.
10x Genomics Chromium Single Cell 3’ (v3 chemistry) system. RNA sequencing on the NovaSeqS4 Illumina achieved an acceptable read depth for each condition (between 27,541-78,121 mean read pairs/cell for 4,613-9,813 cells per condition)

value: brain assembloid

value: iPSC derived

value: hippocampus-like


title: Mut Hc+GE D084


title: Mut Hc+GE D120


title: EPI2_RUN2_GEX

description: Library name: EPI2_RUN2_GEX

value: EPCAM+


title: Mut Cx+GE D120

value: forebrain-like


title: EPI1_RUN2_HTO

description: Library name: EPI1_RUN2_HTO

value: Small Intestine

value: 5' Chemistry, 10x


title: EPI1_RUN1_HTO

description: Library name: EPI1_RUN1_HTO

value: Feature Barcoding

value: HTO4:Inf.N.Inv, GI 6788, HTO2:Fist.N.Inv, TIP 473, HTO1:Fist.Inv, TIP 473, HTO5:HC, TIP 522, HTO3:Inf.Inv, GI6788


title: EPI1_RUN2_TCR

description: Library name: EPI1_RUN2_TCR

value: VDJ Profiling

value: Crohn's Disease


title: EPI1_RUN1_TCR

description: Library name: EPI1_RUN1_TCR


title: iCtrl Cx+GE D120


title: iCtrl Hc+GE D120


title: STR2_Levicell_HTO

description: Library name: STR2_Levicell_HTO

value: CD45- EPCAM-


title: hTERT1-RPE1, SMC3, RB KO, clone 1.7, G1

city: Boston

first: Hanjun

last: Lee

state: Massachusetts

address: 77, Avenue Louis Pasteur

department: Department of Genetics

institute: Harvard Medical School

library_source: genomic

data_processing:
Adapter trimming was performed using trim-galore in a paired-end mode to remove Illumina adapter sequences.
Sequencing reads were then aligned using bwa mem (v0.7.17-r1188) either to the hg38 human reference genome build or the chimera build of hg38 human reference genome build and NZ_CP080620.1 Escherichia coli TOP10 strain reference genome build.
After the aligned .bam file was sorted and indexed using samtools (v1.10), sambamba (v0.7.1) was utilized to sort, mark duplicate reads, and index .bam files.
Then, we filtered reads in the .bam files to produce a file that only contains reads that are not PCR duplicates, with less than or equal to two mismatches, and with mapping quality that is greater than or equal to 30.
After indexing the .bam file, deeptools bamCoverage (v3.5.1) was utilized to normalize the number of reads based on counts per million (CPM), and .bigWig files were generated at a 1 bp resolution. For samples with spike-in controls, spike-in normalization was performed by multiplying the data column in each bedGraph file with a scaling factor. The scaling factor was determined by dividing the number of reads that are aligned to the NZ_CP080620.1 Escherichia coli TOP10 strain reference genome build by the total number of aligned reads and further multiplying the value by 1,000,000 and rounding it.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: All cells were cultured at 37ºC with 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 25 mM glucose, 2 mM glutamine, 5% fetal bovine albumin, and antibiotics (penicillin, 100 units/mL; streptomycin, 100 μg/mL).

extract_protocol:
ChIP assays were carried out on hTERT1-RPE1 cell cultures using approximately 5 million cells per sample and per epitope. Cells were washed once with PBS and fixed with 1.5 mM ethylene glycol bis(succinimidyl succinate) (Thermo Scientific, Cat. # 21565) for 30 min at 25ºC and 1% formaldehyde (Sigma, Cat. # F8775) for 10 min at 37ºC. 20 mM Tris-HCl (pH 7.5) and 150 mM glycine were used to quench cross-linking. Cell pellets were washed twice with ice-cold PBS, and lysates were prepared using 300 μL lysis buffer (50mM Tris-HCl (pH 7.4), 1% SDS, and 0.25% DOC) supplemented with protease and phosphatase inhibitors cocktail (PPI) (Thermo Scientific, Cat. # 78442) for 10 min on ice.
Cell lysates were diluted with 900 μL ChIP dilution buffer (50mM Tris-HCl (pH 7.4), 0.1% SDS, 150 mM NaCl, and 1.84% Triton-X) supplemented with PPI. Chromatin was fragmented to a size of 200–700 bases with Branson 250 sonifier. Solubilized chromatin was further diluted with 1800 μL ChIP dilution buffer and immunoprecipitated with the indicated antibodies overnight at 4°C. The primary antibodies were utilized for ChIP: anti-SMC3 (Abcam, Cat. # ab9263, RRID: AB_307122) anti-acSMC3 K105/K106 (Sigma-Aldrich, Cat. # MABE1073), anti-H3K27ac (Active Motif, Cat. # 39034, RRID: AB_2722569), and anti-H3K27me3 (Cell Signaling Technology, Cat. # 12158, RRID: AB_2797834). Antibody-chromatin complexes were pulled down with protein G-Dynabeads (Life Technologies, Cat. # 10004D) for 2 hours at 4°C and washed 3 times with RIPA 150 Wash Buffer (0.1% SDS, 0.1% DOC 1% Triton X-100, 1 mM EDTA, 10 mM Tris-HCl (pH 8), and 150mM NaCl), 3 times with RIPA 500 Wash Buffer (0.1% SDS, 0.1% DOC, 1% Triton X-100, 1 mM EDTA, 10 mM Tris-HCl (pH 8), and 500 mM NaCl), 3 times with LiCl wash buffer (10 mM Tris-HCl (pH 8), 250 mM LiCl, 0.5% Triton X-100, and 0.5% DOC) and once with ice-cold 10 mM Tris-HCl (pH 8). Chromatin complexes were eluted from the beads using elution buffer (10 mM Tris-HCl (pH 8), 0.1% SDS, 150 mM NaCl, and 5 mM DTT) for 1 hour at 65°C and were treated with RNase A (Roche, Cat. # 11119915001) for 30 min at 37°C. Proteinase K (Thermo Scientific, Cat. # 25530049) treatment and reverse cross-linking was performed for 3 hours at 65°C. After reversal of the crosslinks, immunoprecipitated DNA was extracted with AMP Pure XP beads (Beckman Coulter, Cat. # A63881). ChIP DNA was quantified with Qubit dsDNA HS Assay kit (Thermo Scientific, Cat. # Q32851). 1–2 ng ChIP DNA samples were used to prepare sequencing libraries, using the Ovation Ultralow System V2 kit (TECAN, Cat. # 0344NB-A01).

treatment_protocol: CRISPR/Cas9 targeting exon 1 of the RB1 gene was utilized to prepare a RB KO in hTERT1-RPE1 cells. G1 synchronization was performed via contact inhibition through maintaining cells for 6 d in a confluent state. Cells were subsequently released to S phase via trypsinization. For mitotic synchronization in prometaphase, S phase-synchronized cells were transferred to T175 (large) flasks to sub-confluent state. After 16 h, cells were treated with 0.1 µg/mL nocodazole (Cell signaling, Cat. #2190) for 6 h. Mitotic cells were collected by gentle shaking and tapping of the flask.

value: Retinal pigment epithelium

tag: genotype

value: RB KO

tag: phase


title: hTERT1-RPE1, SMC3, RB KO, M, biol rep 1

value: M


title: STR4_Levicell_HTO

description: Library name: STR4_Levicell_HTO

value: HTO6:Inf.Inv, TIP 651, HTO2:IBD 38, Strict.Inv, HTO3:Healthy, TIP 852, HTO4:Healthy, GI 8366


title: hTERT1-RPE1, INPUT, RB KO, clone 1.7, G1


title: STR3_Levicell_GEX

description: Library name: STR3_Levicell_GEX

value: Gene Expression


title: hTERT1-RPE1, SMC3, RB WT, M, biol rep 2

value: RB WT


title: hTERT1-RPE1, INPUT, RB KO, M


title: G3_Medullo_KD3

city: Napoli

first: Francesco

last: Migliaccio

address: Via Pietro Castellino 111

department: DIETI / IAC

country: Italy

institute: Federico II / IAC

description: GapmeR-transfected D283 Med cells

data_processing:
Trimming with trimgalore-0.6.4_dev
Alignment with STAR 2.7.9a with options:  --outFilterMultimapNmax 20 --outMultimapperOrder Random --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate
RSEM to Quantify transcripts
Assembly: GRCh38.p13, Gencode Release 38, GRCh38.primary_assembly.genome.fa
Supplementary files format and content: tab-delimited text files include rounded row counts values for each Sample

source_name: D283 Med cells

extract_protocol:
miRNeasy Micro Kit (Qiagen)
TruSeq Stranded mRNA Library

treatment_protocol: Rea J, Carissimo A, Trisciuoglio D, Illi B, Picard D, Remke M, Laneve P, Caffarelli E. Identification and Functional Characterization of Novel MYC-Regulated Long Noncoding RNAs in Group 3 Medulloblastoma. Cancers (Basel). 2021 Jul 30;13(15):3853. doi: 10.3390/cancers13153853. PMID: 34359754; PMCID: PMC8345409.

value: D283 Med cells

value: G3 Medulloblastoma

value: KD

value: Cellular transfection using LNA GapmeRs


title: G3_Medullo_KD2

description: GapmeR-transfected D283 Med cells


title: hTERT1-RPE1, SMC3, RB WT, M, biol rep 1


title: hTERT1-RPE1, INPUT, RB WT, M


title: G3_Medullo_KD1

description: GapmeR-transfected D283 Med cells


title: G3_Medullo_SCR2

description: GapmeR-transfected D283 Med cells

value: SCR


title: G3_Medullo_SCR3

description: GapmeR-transfected D283 Med cells


title: Neural precursor cell 608-1 uninfected replicate 1

city: Southampton

first: Rob

last: Ewing

state: Hampshire

address: University Rd, Southampton

department: School of Biological Sciences

institute: University of Southampton

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N6_ZC_1

data_processing:
Assembly: HISAT2
quality control checks on raw sequence data  was performed usingFastQC (V0.11.9-0)
Sequence reads were trimmed for low quality sequences and adapters using Trim galore (version 0.6.6-0)
Reads were aligned against the Homo Sapien GRCh38 and ZIKV BeH819966 genome using HISAT2 (V2.2.0)
Read counts were obtained using FeatureCounts via the Subread package (Version 2.0.6)
Supplementary files format and content: Tab-dellmited text files with raw counts for each sample

source_name: Cerebellum

growth_protocol: monolayer under standard conditions (5% CO2, 37°C)

extract_protocol:
High-quality total RNA was purified using the Monarch Total RNA Miniprep Kit (NEB #T2010S) as per the manufacturer’s protocol
mRNA library preparation (poly A enrichment)

treatment_protocol: Infected at multiplicity of infection (MOI) of 2 for 60 minutes

value: Cerebellum

value: hiPSC-derived NPC from CZS-affected twin

value: WT


title: Neural precursor cell 608-1 ZIKV infection 24 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N6_Z24_3

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: Neural precursor cell 608-1 uninfected replicate 3

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N6_ZC_3


title: Neural precursor cell 608-1 uninfected replicate 2

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N6_ZC_2


title: Neural precursor cell 608-1 ZIKV infection 24 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N6_Z24_1


title: Neural precursor cell 608-1 ZIKV infection 24 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N6_Z24_2


title: hTERT1-RPE1, SMC3, RB KO, M, biol rep 2


title: hTERT1-RPE1, RB KO, G1, HiChIP biol rep 2

data_processing:
*library strategy: HiChIP
Adapter trimming was performed using trim-galore in a paired-end mode to remove Illumina adapter sequences.
Sequencing reads were aligned to the hg38 human reference build using bwa mem (v0.7.17-r1188).
Pairtools (v0.3.0) were utilized to parse, sort, and deduplicate ligation sequencing reads to valid pairs.
Juicer Tools pre (v1.22.01) was utilized to generate .hic files for the chromosome conformation capture maps.
Assembly: hg38
Supplementary files format and content: hic

extract_protocol:
For each reaction, 5,000,000 cells were collected and washed with PBS. Chromatin was crosslinked with 0.3 M disuccinimidyl glutarate (DSG; Thermo Fisher Scientific, Cat. # A35392) and 1% formaldehyde (Sigma-Aldrich, Cat. # F8775).
The HiChIP MNase library was prepared using the Dovetail HiChIP MNase Kit for mammalian cells (Cat. # 21007), according to the manufacturer’s protocol. The cross-linked chromatin was digested in situ with micrococcal nuclease. The MNase reaction was performed using 0.5 μL of MNase enzyme mix in a 100 μL solution of 1X nuclease digest buffer and was stopped by addition of 10 μL of 0.5 M EGTA (Dovetail Mico-C Module Box 2, Cat. # DG-NUC-001). The cross-linked, digested chromatin was then extracted upon cell lysis with 1X RIPA and solubilized with 1 μL of 20% SDS (Dovetail Chromatin Immunoprecipitation Core Box 1, Cat. # DG-NUC-001). Chromatin fragments from 1000 ng of lysates were incubated with 300 ng of antibody against H3K27ac (Cell Signaling, Cat. # 8173) overnight for chromatin immunoprecipitation. The antibody-protein-DNA complex was pulled down with protein A/G-coated beads (Dovetail Chromatin Immunoprecipitation Core Box 1, Cat. # DG-NUC-001). Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends as described by the manufacturer (Dovetail Mico-C Module Box 2, Cat. # DG-NUC-001). After proximity ligation, the crosslinks were reversed, and the associated proteins were degraded by 1X crosslink reversal buffer supplemented with proteinase K (Dovetail Chromatin Immunoprecipitation Core Box 1 and Dovetail Mico-C Module Box 2, Cat. # DG-NUC-001). DNA was purified using SPRI select beads (Beckman Coulter, Cat. # B23317), and then converted into a sequencing library using Illumina-compatible adaptors (Dovetail Dual Index Primer Set #1 for Illumina, Cat. # DG-PRS-002 and Dovetail Library Module for Illumina, Cat. # DG-LIB-001). Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification (Dovetail Chromatin Immunoprecipitation Core Box 1 and Dovetail Mico-C Module Box 2, Cat. # DG-NUC-001). Size selection was performed using SPRIselect beads (Beckman Coulter, Cat. # B23317).

treatment_protocol: CRISPR/Cas9 targeting exon 1 of the RB1 gene was utilized to prepare a RB KO in hTERT1-RPE1 cells. G1 synchronization was performed via contact inhibition through maintaining cells for 6 d in a confluent state.


title: Neural precursor cell 608-1 ZIKV infection 12 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N6_Z12_2

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: Neural precursor cell 608-1 ZIKV infection 12 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N6_Z12_3


title: Neural precursor cell 608-1 ZIKV infection 12 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N6_Z12_1


title: hESC, neural Progenitors, cytoplasm, PANDORA-seq, rep1

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description: Cytoplasm

data_processing:
The raw reads were trimmed by performing SPORTS1.1.2 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Ectoderm progenitors

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Ectoderm progenitors

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: hTERT1-RPE1, RB WT, G1, HiChIP biol rep 2

value: Retinal pigment epithelium


title: hTERT1-RPE1, RB KO, G1, HiChIP biol rep 1

value: RB KO


title: hESC, neural Progenitors, cytoplasm, PANDORA-seq, rep2

description: Cytoplasm


title: hESC, neural Progenitors, cytoplasm, traditional-seq, rep1

description: Cytoplasm

value: The 15-50nt RNAs were sequenced with standard protocols.


title: hESC, neural Progenitors, cytoplasm, traditional-seq, rep2

description: Cytoplasm


title: hESC, neural Progenitors, pbody, PANDORA-seq, rep1

description: Pbody


title: hESC, primed, cytoplasm, PANDORA-seq, rep2

description: Cytoplasm

source_name: Primed ES cells

value: Primed ES cells


title: hESC, neural Progenitors, pbody, traditional-seq, rep1

description: Pbody


title: hESC, primed, pbody, PANDORA-seq, rep1

description: Pbody


title: hESC, primed, cytoplasm, PANDORA-seq, rep1

description: Cytoplasm


title: G3_Medullo_SCR1

description: GapmeR-transfected D283 Med cells


title: hESC, primed, pbody, traditional-seq, rep2

description: Pbody


title: hESC, primed, cytoplasm, traditional-seq, rep1

description: Cytoplasm


title: hESC, primed, pbody, traditional-seq, rep1

description: Pbody


title: hTERT1-RPE1, RB KO

data_processing:
Adapter trimming was performed using trim-galore in a paired-end mode to remove Illumina adapter sequences.
Sequencing reads were then aligned using bwa mem (v0.7.17-r1188) to the hg38 human reference genome build.
After the aligned .bam file was sorted and indexed using samtools (v1.10), sambamba (v0.7.1) was utilized to sort, mark duplicate reads, and index .bam files.
Then, we filtered reads in the .bam files to produce a file that only contains reads that are not PCR duplicates, with less than or equal to two mismatches, and with mapping quality that is greater than or equal to 30. After indexing the .bam file, deeptools bamCoverage (v3.5.1) was utilized to normalize the number of reads based on counts per million (CPM), and .bigWig files were generated at a 1 bp resolution.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
RBWT and RBKO hTERT1-RPE1 cells were harvested from culture, and approximately 5 million cells per sample were utilized. After the chromatin was isolated from cells, the chromatin was digested with micrococcal nuclease.
1–2 ng MNase-digested DNA samples were used to prepare sequencing libraries. The Ovation Ultralow System V2 kit (TECAN, Cat. # 0344NB-A01) was utilized for sequencing library construction.

treatment_protocol: CRISPR/Cas9 targeting exon 1 of the RB1 gene was utilized to prepare a RB KO in hTERT1-RPE1 cells.


title: hTERT1-RPE1, RB WT

value: RB WT


title: hTERT1-RPE1, RB KO, S, biol rep 3

data_processing:
Adapter trimming was performed using trim-galore in a paired-end mode to remove Illumina adapter sequences.
Sequencing reads were then aligned using STAR (v2.7.1a) to the hg38 human reference genome build.
A two-pass alignment pipeline was utilized, where the first pass was performed using the sjdbOverhang of 149 and the sjdbGTFfile from Ensembl (v105) and the second pass was performed using the SJ.out.tab files generated from the first pass alignment.
The calculation of the expression level was performed on individual replicate experiments using the RSEM (v1.3.1) algorithm in a paired-end mode.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells using the Direct-zol RNA MiniPrep Plus kit (Zymo Research, Cat. # R2073).
Multiplexed RNA sequencing libraries were prepared using the TruSeq library prep kit (Illumina, Cat. # RS-122-2301/2), which utilizes Oligo-dT beads to capture polyA tails.

treatment_protocol: CRISPR/Cas9 targeting exon 1 of the RB1 gene was utilized to prepare a RB KO in hTERT1-RPE1 cells. G1 synchronization was performed via contact inhibition through maintaining cells for 6 d in a confluent state. Cells were subsequently released to S phase via trypsinization.

value: S


title: hTERT1-RPE1, RB KO, S, biol rep 2


title: hTERT1-RPE1, RB KO, S, biol rep 1


title: hTERT1-RPE1, RB WT, S, biol rep 3


title: hTERT1-RPE1, RB WT, S, biol rep 2


title: hTERT1-RPE1, RB WT, G1, HiChIP biol rep 1


title: hTERT1-RPE1, RB WT, S, biol rep 1


title: hTERT1-RPE1, RB KO, G1, biol rep 3


title: hTERT1-RPE1, RB KO, G1, biol rep 2


title: hESC, neural Progenitors, pbody, PANDORA-seq, rep2

description: Pbody


title: hTERT1-RPE1, RB KO, G1, biol rep 1


title: hTERT1-RPE1, RB WT, G1, biol rep 1


title: hTERT1-RPE1, RB WT, G1, biol rep 2


title: hESC, neural Progenitors, pbody, traditional-seq, rep2

description: Pbody


title: hESC, primed, pbody, PANDORA-seq, rep2

description: Pbody


title: hTERT1-RPE1, RB WT, G1, biol rep 3


title: hTERT1-RPE1, H3K27me3, RB WT

treatment_protocol: CRISPR/Cas9 targeting exon 1 of the RB1 gene was utilized to prepare a RB KO in hTERT1-RPE1 cells. G1 synchronization was performed via contact inhibition through maintaining cells for 6 d in a confluent state. Cells were subsequently released to S phase via trypsinization. RB1 knockdown or the replacement of endogenous RB with the constitutively active RB (i.e., RB∆CDK) were done in cells transduced with pINDUCER11 (Addgene, Cat. # 44363) or pINDUCER20 (Addgene, Cat. # 44012) constructs. Doxycycline induction was performed by treating cells with doxycycline (Sigma-Aldrich, Cat. # D9891) at 0.5 μg/mL concentration.


title: hESC, primed, cytoplasm, traditional-seq, rep2

description: Cytoplasm


title: hTERT1-RPE1, H3K27ac, RB KO, S


title: hTERT1-RPE1, H3K27ac, RB WT, S


title: hTERT1-RPE1, H3K27ac, RB KO, G1


title: hTERT1-RPE1, H3K27me3, RB dCDK

value: RB dCDK


title: hTERT1-RPE1, acSMC3, RB WT, G1


title: hTERT1-RPE1, H3K27ac, RB WT, G1


title: hTERT1-RPE1, acSMC3, RB KO, G1


title: hTERT1-RPE1, SMC3, RB WT, S, spike-in


title: hTERT1-RPE1, SMC3, RB KO, S, spike-in


title: hTERT1-RPE1, SMC3, RB KO, S


title: hTERT1-RPE1, SMC3, RB KO, G1, biol rep 2


title: hTERT1-RPE1, SMC3, RB KO, G1, spike-in


title: hTERT1-RPE1, SMC3, RB WT, S


title: hTERT1-RPE1, SMC3, RB KO, G1, biol rep 1


title: hTERT1-RPE1, SMC3, RB dCDK, 72 hrs

value: RB dCDK, 72 hrs


title: hTERT1-RPE1, SMC3, RB WT, G1, biol rep 2


title: hTERT1-RPE1, SMC3, RB WT, G1, spike-in


title: hTERT1-RPE1, SMC3, RB dCDK, 24 hrs

value: RB dCDK, 24 hrs


title: hTERT1-RPE1, SMC3, RB WT, G1, biol rep 1


title: hTERT1-RPE1, SMC3, RB dCDK, 0 hr

value: RB dCDK, 0 hr


title: hTERT1-RPE1, INPUT, S


title: hTERT1-RPE1, INPUT, G1


title: hTERT1-RPE1, RB KO, S

data_processing:
Adapter trimming was performed using trim-galore in a paired-end mode to remove Illumina adapter sequences.
Sequencing reads were then aligned using bwa mem (v0.7.17-r1188) to the hg38 human reference genome build.
After the aligned .bam file was sorted and indexed using samtools (v1.10), sambamba (v0.7.1) was utilized to sort, mark duplicate reads, and index .bam files.
Then, we filtered reads in the .bam files to produce a file that only contains reads that are not PCR duplicates, with less than or equal to two mismatches, and with mapping quality that is greater than or equal to 30.
After indexing the .bam file, deeptools bamCoverage (v3.5.1) was utilized to normalize the number of reads based on counts per million (CPM), and .bigWig files were generated at a 1 bp resolution.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
For each reaction, 100,000 cells were collected and washed with PBS. Cells were resuspended in cold lysis buffer provided by the ATAC-seq kit (Active Motif, Cat. # 53150) and centrifuged at 1000xg for 10 min at 4°C.
The nuclei pellet was resuspended in the tagmentation buffer provided by the ATAC-seq kit (Active Motif Cat. # 53150) and the reaction was incubated at 37°C for 30 min. Tagmented DNA was purified and used to generate sequencing libraries following the manufacturer’s instructions.


title: hTERT1-RPE1, RB WT, G1


title: hTERT1-RPE1, RB KO, G1


title: hTERT1-RPE1, RB dCDK, 72 hrs


title: hTERT1-RPE1, RB dCDK, 0 hr


title: hTERT1-RPE1, RB WT, asynchronous


title: hTERT1-RPE1, RB WT, S


title: PBMDSC_3 (3408)

city: Minneapolis

first: Michael

last: Zaiken

state: MN

address: East River Parkway

department: Pediatrics

institute: University of Minnesota

data_processing:
Indexed libraries were normalized, pooled, and loaded onto a NovaSeq paired end flow cell for clustering and sequencing using Illumina’s bcl2fastq v2.20.
FASTQ reads were entered into the Collection of Hierarchical UMII/RIS Pipelines for quality control, trimming, confirming viability.
aligning reads using HISAT234
filtering alignments using SAMtools
generating output matrices using Subread FeatureCounts.
Assembly: Hg38 reference genome (GRCh38)
Supplementary files format and content: Comma seperated value (csv) file with raw counts for each sample

source_name: peripheral blood

extract_protocol:
Cells were freshly harvested from the culture before RNA collection. CD14+ and CD14- iMDSC samples were flow-sorted based on CD14 expression. LPS + ATP treated MDSCs, prepared as above, were first resuspended with 2-mercaptoethanol (Sigma-Aldrich: M6250) in lysis buffer (PureLink RNA Mini Kit, Invitrogen: 12183018A). Samples were frozen on dry ice until processing at Fate Therapeutics (San Diego, CA). RNA was collected, isolates quantified by fluorometric RiboGreen assay, integrity determined using capillary electrophoresis and samples converted to sequencing libraries using Takara Bio’s SMARTer Stranded Total RNA-Seq–Pico Mammalian Kit v2 (634414).
Samples converted to sequencing libraries using Takara Bio’s SMARTer Stranded Total RNA-Seq–Pico Mammalian Kit v2 (634414).

treatment_protocol: LPS and ATP treatment: MDSCs were harvested and washed with PBS (Corning: 21-031-CV) twice. Then MDSCs were treated with LPS (0.2 ug/ml, Invivogen: TLRL-PEKLPS) and ATP (2 mM, Thermo Fisher: R0441) for 2h and 0.5h, respectively.

value: peripheral blood

value: PBMC derived MDSC

value: Non treated


title: hTERT1-RPE1, RB dCDK, 24 hrs


title: hTERT1-RPE1, RB KO, asynchronous


title: PBMDSC_2 (3407)

value: WT


title: PBMDSC_1 (3406)


title: LPSplusATP_PBMDSC_3 (3428)

value: LPS and ATP treated


title: PBMDSC_4 (3409)


title: LPSplusATP_IMDSC_3 (3432)

source_name: not applied

value: not applied

value: IPSC derived MDSC


title: LPSplusATP_PBMDSC_1 (3426)


title: LPSplusATP_IMDSC_4 (3433)


title: LPSplusATP_IMDSC_1 (3430)


title: LPSplusATP_PBMDSC_2 (3427)


title: CD14pos_KS010_4 (3425)


title: LPSplusATP_IMDSC_2 (3431)


title: CD14pos_KS010_3 (3424)


title: CD14pos_AM013_4 (3417)


title: CD14pos_AM013_3 (3416)


title: CD14pos_AM013_2 (3415)


title: CD14pos_KS010_2 (3423)


title: CD14pos_KS010_1 (3422)


title: CD14pos_AM013_1 (3414)


title: CD14neg_AM013_4 (3421)


title: CD14neg_AM013_2 (3419)


title: CD14neg_AM013_3 (3420)


title: CD14neg_AM013_1 (3418)


title: AM013_4 (3413)


title: AM013_2 (3411)


title: AM013_3 (3412)


title: LPSplusATP_PBMDSC_4 (3429)


title: AM013_1 (3410)


title: QBC-939 cells, Control-rep2

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

institute: Qilu Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: hg19
Supplementary files format and content: 1_genes_fpkm_expression.xlsx

source_name: CCA Tumor

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Bile Duct Cancer (Cholangiocarcinoma)

value: CCA Tumor

value: control


title: QBC-939 cells, Control-rep3


title: QBC-939 cells, Control-rep4


title: QBC-939 cells, Control-rep1


title: QBC-939 cells, kdSMAD4-rep4

value: SMAD4 knockdown


title: QBC-939 cells, kdSMAD4-rep3


title: QBC-939 cells, kdSMAD4-rep2


title: QBC-939 cells, kdSMAD4-rep1


title: QBC-939 cells,CRISPR screen,Histamine processed,rep6

data_processing:
Filter and quality control raw data to ensure the accuracy of sequencing data;
Screening for sequencing reads is compared to sgRNA sequences in sgRNA libraries;
The sgRNA and gene reads enrichment of each sample were counted, and the sample quality control was carried out after standardization;
Comparisons of sgRNAs between groups and screening of essential genes were performed, and functional enrichment of related genes was analyzed.
Assembly: mm10
Library strategy: Genome-wide CRISPR screen

extract_protocol:
We used CRISPR-PoolTMKOUT-Human-Single vector to build GeCKO(genome-scale CRISPR-Cas9 knockout) human library in QBC-939(CCA cell line),the nuclear genome was extracted for PCR(Polymerase Chain Reaction) purification and amplification.
The PCR amplification products were detected by Genome-wide CRISPR screen.

value: cholangiocarcinoma (CCA)

value: Histamine


title: QBC-939 cells,CRISPR screen,Histamine processed,rep4


title: QBC-939 cells,CRISPR screen,control,rep6


title: QBC-939 cells,CRISPR screen,Histamine processed,rep1


title: QBC-939 cells,CRISPR screen,Histamine processed,rep2


title: QBC-939 cells,CRISPR screen,Histamine processed,rep5


title: QBC-939 cells,CRISPR screen,control,rep5


title: QBC-939 cells,CRISPR screen,Histamine processed,rep3


title: MDD_5B

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

description: 150x150 pair-ended mode

data_processing:
For RNA-seq, the Read 2 received from sequencing was processed by extracting the UMI, Barcode A and Barcode B. The processed Read 1 was trimmed, mapped against the human genome (GRCh38), de-multiplexed and annotated using the ST pipeline v1.8.1 (Benitez et al., PLOS ONE, 2017), which generated the digital gene expression matrix for down-stream analysis. The rows of the gene matrix correspond to pixels, defined by their location info (barcode A x barcode B) and columns correspond to genes.
Assembly: GRCh38
Supplementary files format and content: Spatial mRNA-seq expression matrix of each sample. File format (.tsv): tab-delimited text files include counts for each pixel.

source_name: Hippocampus (Brain)

extract_protocol:
The flash-frozen human hippocampus brain slides were taken from the -80˚C freezer and placed on a bench at room temperature for about 10 minutes. 1X phosphate buffer saline (PBS) supplemented with RNase inhibitor (0.05U/µL, Enymatics) was used to wash the tissue. Following this, they were fixed with 4% formaldehyde (Sigma) for 20 minutes at room temperature. The tissues were once again cleaned with the RNase inhibitor (0.05U/µL) in PBS, and then permeabilized with 1% Triton X-100 in PBS. Afterwards, the tissue slides were dipped in diH2O and then gently dried with nitrogen air.
MRNA library was contructed following our DBiT-seq protocol (Liu et al., Cell, 2020) (https://doi.org/10.1016/j.cell.2020.10.026).

value: Hippocampus (Brain)

tag: donor id

tag: group

value: MDD


title: QBC-939 cells,CRISPR screen,control,rep1


title: QBC-939 cells,CRISPR screen,control,rep4


title: QBC-939 cells,CRISPR screen,control,rep3


title: QBC-939 cells,CRISPR screen,control,rep2


title: MDD_4B

description: 150x150 pair-ended mode


title: MDD_3B

description: 150x150 pair-ended mode


title: MDD_4A

description: 150x150 pair-ended mode


title: MDD_1A

description: 150x150 pair-ended mode


title: CTRL_6A

description: 150x150 pair-ended mode

value: CTRL


title: MDD_3A

description: 150x150 pair-ended mode


title: CTRL_4B

description: 150x150 pair-ended mode


title: CTRL_4A

description: 150x150 pair-ended mode


title: CTRL_2A

description: 150x150 pair-ended mode


title: CTRL_3A

description: 150x150 pair-ended mode


title: 200810876-09

type: genomic

city: Miami

first: Lily

last: Wang

address: 1120 NW 14th St

institute: University of Miami

description: study sample

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Standard recommended Illumina scanner setting.

data_processing:
idat files were read using minfi::read.metharray.exp, converted to beta values with minfi::getBeta
beta.csv contains beta values

label: Cy3 and Cy5

source_name: Blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).

value: Blood

tag: batch

value: B


title: CTRL_1A

description: 150x150 pair-ended mode


title: 201104164-02

description: study sample


title: ATAC_MDD_3C

description: 150x150 pair-ended mode

data_processing:
For ATAC-seq, data was aligned using the Cell Ranger ATAC software (v2.1) developed by 10X Genomic to produce the processed fragment file. Open chromatin region peaks were called on fragment files merged from all samples using MACS2 peak caller (Zhang et al., Genome Biology, 2008). Peaks  overlapping with ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. Peak summits were extended by 250 bp on each side and defined as accessible regions.
Assembly: GRCh38
Supplementary files format and content: Spatial-ATAC-seq fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

extract_protocol:
The flash-frozen human hippocampus brain slides were taken from the -80˚C freezer and placed on a bench at room temperature for about 10 minutes. 1X phosphate buffer saline (PBS) supplemented with RNase inhibitor (0.05U/µL, Enymatics) was used to wash the tissue. Following this, they were fixed with 4% formaldehyde (Sigma) for 20 minutes at room temperature. The tissues were once again cleaned with the RNase inhibitor (0.05U/µL) in PBS, and then permeabilized with 1% Triton X-100 in PBS. Afterwards, the tissue slides were dipped in diH2O and then gently dried with nitrogen air.
Open chromatin library by ATAC-seq was constructed following spatial-ATAC-seq protocol (Deng et al., Nature, 2022) (DOI: 10.1038/s41586-022-05094-1).


title: 200810435-07

description: study sample


title: 200810854-07

description: study sample


title: 200810700-09

description: study sample


title: 200911583-04

description: study sample


title: 200810359-08

description: study sample


title: 201011464-02

description: study sample


title: 200900580-07

description: study sample


title: 201104309-02

description: study sample


title: 200810312-08

description: study sample


title: 200810430-09

description: study sample


title: 201011458-02

description: study sample


title: 200810879-07

description: study sample


title: 200810607-08

description: study sample


title: 200817559-04

description: study sample


title: 200810499-08

description: study sample


title: CTRL_5A

description: 150x150 pair-ended mode


title: 200810685-07

description: study sample


title: 200900627-07

description: study sample


title: 200810875-07

description: study sample


title: 200810388-08

description: study sample


title: 200810958-08

description: study sample


title: 200810618-07

description: study sample


title: 200810341-09

description: study sample


title: 201104023-02

description: study sample


title: 200810620-07

description: study sample


title: 201104195-02

description: study sample


title: 200810873-07

description: study sample


title: 200810315-07

description: study sample


title: 200810814-07

description: study sample


title: 200810672-07

description: study sample


title: 201011550-02

description: study sample


title: 200810537-07

description: study sample


title: 200811015-09

description: study sample


title: 200810355-08

description: study sample


title: 200900587-11

description: study sample


title: 200810802-07

description: study sample


title: 200810425-08

description: study sample


title: 200810657-07

description: study sample


title: 200810564-07

description: study sample


title: 200900670-11

description: study sample


title: 200817540-05

description: study sample


title: 200810586-07

description: study sample


title: 200900585-11

description: study sample


title: 200810365-10

description: study sample


title: 200810907-08

description: study sample


title: 200810580-07

description: study sample


title: 200810779-07

description: study sample


title: 200810951-08

description: study sample


title: 200817736-04

description: study sample


title: 200810939-08

description: study sample


title: 200811010-07

description: study sample


title: 200810279-10

description: study sample


title: 200810961-07

description: study sample


title: 200811027-07

description: study sample


title: 200810971-07

description: study sample


title: 200810774-08

description: study sample


title: 200810641-07

description: study sample


title: 200810972-08

description: study sample


title: 200912309-04

description: study sample


title: 200810764-08

description: study sample


title: 200810642-07

description: study sample


title: 200810964-07

description: study sample


title: 200810934-07

description: study sample


title: 200810461-07

description: study sample


title: 200810995-08

description: study sample


title: 201104176-02

description: study sample


title: 201104010-03

description: study sample

value: A


title: 200810438-08

description: study sample


title: 200810526-07

description: study sample


title: 200810630-11

description: study sample


title: 200810451-08

description: study sample


title: 200810479-09

description: study sample


title: 200810500-08

description: study sample


title: 200810264-09

description: study sample


title: 201103855-02

description: study sample


title: 200900620-11

description: study sample


title: 200810678-08

description: study sample


title: 200810592-10

description: study sample


title: 201103976-02

description: study sample


title: 200817747-04

description: study sample


title: 200810560-08

description: study sample


title: 200810597-07

description: study sample


title: 200810670-08

description: study sample


title: 200900665-08

description: study sample


title: 200810305-09

description: study sample


title: 200900602-08

description: study sample


title: 200810546-07

description: study sample


title: 200810574-07

description: study sample


title: 200810959-07

description: study sample


title: 200810288-09

description: study sample


title: 201104081-02

description: study sample


title: 200810948-08

description: study sample


title: 200810783-08

description: study sample


title: 201103907-02

description: study sample


title: 201103980-02

description: study sample


title: 200810432-09

description: study sample


title: 200810275-08

description: study sample


title: 200810454-08

description: study sample


title: 200810881-09

description: study sample


title: 200811022-07

description: study sample


title: 200810612-08

description: study sample


title: 200810571-07

description: study sample


title: 200810625-09

description: study sample


title: 200900634-09

description: study sample


title: 201104045-02

description: study sample


title: 200810874-07

description: study sample


title: 200810646-08

description: study sample


title: 200810746-07

description: study sample


title: 200811023-07

description: study sample


title: 200811024-07

description: study sample


title: 200810309-09

description: study sample


title: 200810943-07

description: study sample


title: 200811192-08

description: study sample


title: 200810691-08

description: study sample


title: 200810898-07

description: study sample


title: 200810650-07

description: study sample


title: 200810608-09

description: study sample


title: 201104121-02

description: study sample


title: 200810996-07

description: study sample


title: 200810285-08

description: study sample


title: 200811079-08

description: study sample


title: 200810552-07

description: study sample


title: 200810662-08

description: study sample


title: 200810621-08

description: study sample


title: 200810459-07

description: study sample


title: HEK293T cells, siRNA control, cytoplasmic RNA, bio rep 3

city: Bunkyo-ku

first: Tatsuya

last: Ishizuka

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

description: Library name: cytoC_3

data_processing:
Trimmed reads were aligned using HISAT2 and gene expression levels were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM quantification data

extract_protocol:
Total RNA was extracted from HEK293T cells using RNA Premium Kit (Fastgene) following manufacturer's instructions.
Nuclear and cytoplasmic RNA fractions were isolated using the PARIS Kit (Thermo Fisher Scientific) following manufacturer's instructions.
Poly-A selection and cDNA preparation was performed by BGI.

tag: sirna

value: siRNA control


title: 200817561-04

description: study sample


title: 200810623-08

description: study sample


title: HEK293T cells, siRNA control, cytoplasmic RNA, bio rep 2

description: Library name: cytoC_2


title: 201103781-02

description: study sample


title: HEK293T cells, siRNA control, cytoplasmic RNA, bio rep 1

description: Library name: cytoC_1


title: 200810997-08

description: study sample


title: 200810261-08

description: study sample


title: 201104140-03

description: study sample


title: HEK293T cells, FAM32A siRNA, cytoplasmic RNA, bio rep 3

description: Library name: cytoF_3

value: FAM32A siRNA


title: 200810950-08

description: study sample


title: HEK293T cells, FAM32A siRNA, cytoplasmic RNA, bio rep 2

description: Library name: cytoF_2


title: HEK293T cells, FAM32A siRNA, cytoplasmic RNA, bio rep 1

description: Library name: cytoF_1


title: 201104386-03

description: study sample


title: HEK293T cells, siRNA control, nuclear RNA, bio rep 2

description: Library name: nucC_2


title: HEK293T cells, siRNA control, nuclear RNA, bio rep 3

description: Library name: nucC_3


title: 200810638-07

description: study sample


title: 201104276-02

description: study sample


title: 200810924-07

description: study sample


title: HEK293T cells, FAM32A siRNA, nuclear RNA, bio rep 2

description: Library name: nucF_2


title: 200811009-07

description: study sample


title: 200811025-08

description: study sample


title: 200810936-08

description: study sample


title: HEK293T cells, FAM32A siRNA, 24 hours, bio rep 3

description: Library name: FAM32A_24h_3


title: 201104199-02

description: study sample


title: HEK293T cells, FAM32A siRNA, 24 hours, bio rep 1

description: Library name: FAM32A_24h_1


title: 201104320-05

description: study sample


title: HEK293T cells, siRNA control, 24 hours, bio rep 2

description: Library name: NT24h_2


title: 201104131-02

description: study sample


title: HEK293T cells, siRNA control, 24 hours, bio rep 1

description: Library name: NT24h_1


title: CTRL_4

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

description: Library name: Sample8

data_processing:
Low quality nucleotides were removed Illumina fastq filterer/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: mm10
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file. The read counts have been size-factor normalized in DESeq2

organism: Mus musculus

source_name: Subcutaneous Adipose Tissue

growth_protocol: APs were cultured for 1 week in 10 % FBS DMEM 4.5 g/L  glucose.

extract_protocol:
RNA was isolated with a Macherey-Nagel kit
RNA-seq

treatment_protocol: Treatment with IL4 (20 ng/ml) in 1 % FBS DMEM for 4 h.

value: Subcutaneous Adipose Tissue

value: Adipocyte Progenitors

value: WT


title: 201104284-07

description: study sample


title: CTRL_3

description: Library name: Sample7


title: 201104006-03

description: study sample


title: 201103950-05

description: study sample


title: 200810600-07

description: study sample


title: 201104116-02

description: study sample


title: 200810713-08

description: study sample


title: CTRL_1

description: Library name: Sample5


title: HEK293T cells, FAM32A siRNA, nuclear RNA, bio rep 3

description: Library name: nucF_3


title: 201103941-04

description: study sample


title: HEK293T cells, FAM32A siRNA, nuclear RNA, bio rep 1

description: Library name: nucF_1


title: HEK293T cells, siRNA control, nuclear RNA, bio rep 1

description: Library name: nucC_1


title: IL4_4

description: Library name: Sample4


title: IL4_3

description: Library name: Sample3


title: 201104300-02

description: study sample


title: HEK293T cells, siRNA control, 24 hours, bio rep 3

description: Library name: NT24h_3


title: 201011498-04

description: study sample


title: HEK293T cells, FAM32A siRNA, 24 hours, bio rep 2

description: Library name: FAM32A_24h_2


title: IL4_2

description: Library name: Sample2


title: IL4_1

description: Library name: Sample1


title: 201011474-04

description: study sample


title: 201104022-06

description: study sample


title: 201011441-04

description: study sample


title: CUT-Tag_L-GMP_4S-A_GABPA_2

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

description: Library name: Sample12

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: Bone marrow

extract_protocol:
The CUT&Tag assay was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein) according to the manufacturer’s protocol. 5,000-10,000 L-GMPs were harvested and resuspended in 45 µL wash buffer. Then 6 µL ConA beads were added to the sample and incubated at 37°C for 10 min. Then the supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL antibody buffer (20 mM Hepes, pH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1× PIC).
Then, 0.5 µL antibody was added to the sample and incubated at 4°C overnight. The supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL secondary antibody buffer, containing 0.5 µL goat anti-rabbit IgG antibody. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL ChiTag Buffer, containing 0.5 µL ChiTag transposome. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL tagmentation buffer. Then, 1 µL 10% SDS was added to the sample and incubated at 55°C for 10 min, and DNA was extracted using 2×DNA clean beads (Vazyme) and amplified with i5 and i7 primers (Vazyme) by 17-20 PCR cycles. The libraries were purified by 1.2×DNA clean beads (Vazyme).

treatment_protocol: L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Wild-type (WT) and Dek-Ser306A/Ser308A/Ser311A/Ser312A(4S-A) AML mice were sorted, followed by DEK-CUT-Tag-seq. L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven WT AML mice were sorted, followed by PBX3-CUT-Tag-seq. L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven WT,  Dekfl/fl,MX1-Cre (KO) and 4S-A AML mice were sorted, followed by GABPA-CUT-Tag-seq.

value: Bone marrow

value: Leukemia stem cell


title: 201011398-10

description: study sample


title: CTRL_2

description: Library name: Sample6


title: CUT-Tag_L-GMP_4S-A_GABPA_1

description: Library name: Sample11


title: 201007506-03

description: study sample


title: 200900676-14

description: study sample


title: 200900667-14

description: study sample


title: CUT-Tag_L-GMP_WT_GABPA_2

description: Library name: Sample8

value: Wild-type


title: CUT-Tag_L-GMP_WT_GABPA_1

description: Library name: Sample7


title: 200900650-13

description: study sample


title: CUT-Tag_L-GMP_KO_GABPA_1

description: Library name: Sample9


title: 200900664-10

description: study sample


title: 201103734-07

description: study sample


title: 200900609-14

description: study sample


title: CUT-Tag_L-GMP_WT_PBX3_2

description: Library name: Sample6


title: CUT-Tag_L-GMP_4S-A _DEK_2

description: Library name: Sample4


title: CUT-Tag_L-GMP_WT_PBX3_1

description: Library name: Sample5


title: 200900598-11

description: study sample


title: 200900643-10

description: study sample


title: 200811196-07

description: study sample


title: 201011481-05

description: study sample


title: CUT-Tag_L-GMP_4S-A_DEK_1

description: Library name: Sample3


title: 200811045-13

description: study sample


title: CUT-Tag_L-GMP_WT_DEK_2

description: Library name: Sample2


title: 200811034-09

description: study sample


title: LR_PBS5

city: tianjin

first: hui

last: zhang

address: No. 251 Fukang Road, Nankai District

department: eye institute

institute: Tianjin Medical University Eye Hospital

description:
Library name: sample 8
control group, replicate biosample 4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: retina

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: retina


title: CUT-Tag_L-GMP_WT_DEK_1

description: Library name: Sample1


title: CUT-Tag_L-GMP_KO_GABPA_2

description: Library name: Sample10


title: LR_PBS4

description:
Library name: sample 7
control group, replicate biosample 3


title: 200811008-10

description: study sample


title: LR_PBS1

description:
Library name: sample 5
control group, replicate biosample 1


title: 200811000-09

description: study sample


title: 200810993-10

description: study sample


title: LR_sIVs4

description:
Library name: sample 3
sIVs group, replicate biosample 3


title: 200810990-10

description: study sample


title: 200810937-09

description: study sample


title: 200810933-08

description: study sample


title: 200810922-11

description: study sample


title: 200810916-08

description: study sample


title: 200811194-09

description: study sample


title: rd10_PBS2

description:
Library name: sample 6
control group, replicate biosample 2


title: rd10_PBS4


title: 200810904-09

description: study sample


title: rd10_PBS1


title: rd10_PBS3


title: LR_sIVs1

description:
Library name: sample 1
sIVs group, replicate biosample 1


title: rd10_sIVs5

description:
Library name: sample 4
sIVs group, replicate biosample 4


title: 200811020-08

description: study sample


title: rd10_sIVs4


title: 200810882-11

description: study sample


title: LR_PBS3


title: LR_sIVs5


title: rd10_sIVs2


title: 200810913-09

description: study sample


title: 200810880-09

description: study sample


title: 200810903-07

description: study sample


title: 200810861-08

description: study sample


title: 200810863-11

description: study sample


title: LR_sIVs3

description:
Library name: sample 2
sIVs group, replicate biosample 2


title: rd10_sIVs3


title: 200810856-09

description: study sample


title: APBS

city: Chengdu

first: Li

state: None Selected

address: No. 17, Block 3rd, Renmin Road South,

institute: National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University

description:
Library name: Sample 1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/piplines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and dissociated using Collagenase Ⅰ (Sigma, V900891-100MG) and Collagenase Ⅱ (Sigma, V900892-100MG) as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using Fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 (Gibco 11875119) and then resuspended at 1×106 cells per ml in RPMI1640 and 2% FBS (Gibco 10100147C).
Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics Catalog No.1000268). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then loaded to the sample well in Chromium Next GEM Chip G. Subsequently Gel Beads and Partitioning Oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 53℃for 45 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme N411-01), analyzed by Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The libraries were then sequenced on illumina NovaSeq 6000 with PE150 read length.

value: Skeletal muscle

tag: age

value: 18-22 months old


title: 200810842-08

description: study sample

tag: tissue


title: YPBS

description:
Library name: Sample 2
10x Genomics

value: 6-8 weeks old


title: AVac

description:
Library name: Sample 3
10x Genomics


title: YVac

description:
Library name: Sample 4
10x Genomics


title: 200810840-12

description: study sample


title: ATAC_L-GMP_KO_1

description: Library name: Sample3

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 5,000 cells were resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Dekfl/fl(FL) and Dekfl/fl,MX1-Cre (KO) AML mice were sorted, followed by ATAC-seq


title: 200810823-09

description: study sample


title: ATAC_L-GMP_KO_2

description: Library name: Sample4


title: L-GMP_KO_3

description: Library name: Sample7

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Raw read counts per gene were quantified with HTSeq (v0.13.5). Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts per gene for each sample

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: L-GMP(Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Dekfl/fl(FL) and Dekfl/fl,MX1-Cre (KO) AML mice were sorted, followed by RNA-seq


title: 200810817-07

description: study sample


title: 200810807-08

description: study sample


title: L-GMP_KO_4

description: Library name: Sample8


title: 200810796-10

description: study sample


title: 200810794-09

description: study sample


title: 200810772-10

description: study sample


title: 200810780-08

description: study sample


title: 200810762-07

description: study sample


title: ATAC_L-GMP_FL_2

description: Library name: Sample2

value: Dekfl/fl


title: L-GMP_KO_2

description: Library name: Sample6


title: 200810738-10

description: study sample


title: L-GMP_KO_1

description: Library name: Sample5


title: L-GMP_FL_2

description: Library name: Sample2


title: L-GMP_FL_4

description: Library name: Sample4


title: L-GMP_FL_3

description: Library name: Sample3


title: 200810742-11

description: study sample


title: ATAC_L-GMP_FL_1

description: Library name: Sample1


title: L-GMP_FL_1

description: Library name: Sample1


title: 200810734-07

description: study sample


title: 200810720-09

description: study sample


title: 200810717-10

description: study sample


title: 200810715-12

description: study sample


title: Group 3 - MC38 + NIH3T3 Aebp1 KO_CD45cleanup_15b

city: South San Francisco

first: Heyuan

last: Li

address: 213 E Grand Ave

institute: Merck Research Laboratories

description:
Library name: 10
10x Genomics

data_processing:
Sequencing reads were demultiplexed using Cell Ranger v.7.0.1 with default specifications of “mkfastq”. Individual sample gene expression matrices were generated using the Cell Ranger v.7.0.1 “count” against mouse mm10 genome (annotation correspond to Ensembl v.93). Intron reads were included using the argument “—include-introns true”.
Assembly: GRCm38
Supplementary files format and content: Rds file of Seurat object containing raw counts, normalized counts, and clustering

source_name: subcutanuous tumor

growth_protocol: Female C57BL/6 mice at 6-8 weeks of age were inoculated subcutaneously in the lower right flank with a single-cell suspension of 1x106 MC38 tumor cells only and with or without 2x106 AEBP1-WT/AEBP1-KO NIH-3T3 cells suspended in DMEM media (Gibco, 11885084). Tumor progression was monitored using a caliper, and tumor volume was calculated using the formula: 0.5 × length × width2, where the length was the longer dimension.

extract_protocol:
Fresh tumor was cut into approximately 1 mm3 pieces in serum free DMEM, and transferred into C-tube (Miltenyi, 130-096-334) with 5 ml of digestion medium containing collagenase D (0.5 mg/mL, Sigma, 11088882001), dispase (0.5 mg/mL, Gibco, 17105-941), and DnNase I (0.2 mg/mL, Worthington, LS002145) in DMEM. Tissues were incubated for 40 min at 37⁰C shaking withat 200 rpm, then further digested on gentleMACS selecting “imp_mouse_Tumor1” protocol. Afterward, the samples were filtered using a 40 µm cell strainer (Fisherbrand, 22-363-547) and then EDTA was added at 10 mM final concentration. Following the centrifugation at 500g for 5 min, the supernatants were discarded, and the pellets were resuspended with 1 mL PBS containing 2% FBS and 1mM EDTA after washing twice with PBS. Quantified cells are loaded to 10X Genomics Chromium X for single cell capture using 10X Genomics Single Cell 3’ HT GEM Kit v3.1 (PN-1000351) and 3’ HT Gel Bead Kit v3.1 (PN-1000350).
cDNA library preparation was carried out using 10X Genomics Library Construction Kit (PN-1000352). Quality control and quantification of amplified cDNA libraries and final sequencing libraries were performed using a Qubit High Sensitivity ds DNA and Agilent Bioanalyzer DNA High Sensitivity Chip analysis. Libraries were normalized to 4nM concentration and pooled. The pooled libraries were paired end sequenced on NovaSeq S4 platform targeting an average sequencing depth of 50,000 reads per cell.

value: subcutanuous tumor

tag: cell line

value: Aebp1 KO

tag: strain

tag: Sex

value: Female


title: 200810714-11

description: study sample

value: Blood


title: Group 3 - MC38 + NIH3T3 Aebp1 KO_CD45cleanup_16b

description:
Library name: 11
10x Genomics

tag: cell type


title: Group 3 - MC38 + NIH3T3 Aebp1 KO_CD45cleanup_17b

description:
Library name: 12
10x Genomics


title: Group 2 - MC38 + NIH3T3 wt_CD45cleanup_14b

description:
Library name: 9
10x Genomics


title: Group 2 - MC38 + NIH3T3 wt_CD45cleanup_13b

description:
Library name: 8
10x Genomics


title: 200810698-13

description: study sample


title: 200810653-09

description: study sample


title: Group 3 - MC38 + NIH3T3 Aebp1 KO_precleaned_17

description:
Library name: 7
10x Genomics


title: Group 3 - MC38 + NIH3T3 Aebp1 KO_precleaned_16

description:
Library name: 6
10x Genomics


title: 200810639-10

description: study sample


title: 200810631-11

description: study sample


title: Group 2 - MC38 + NIH3T3 wt_precleaned_13

description:
Library name: 3
10x Genomics


title: Group 2 - MC38 + NIH3T3 wt_precleaned_14

description:
Library name: 4
10x Genomics


title: 200810614-11

description: study sample


title: 200810616-11

description: study sample


title: 200810655-15

description: study sample


title: Group 1 - MC38_precleaned_11

description:
Library name: 1
10x Genomics


title: 200810576-10

description: study sample


title: 200810575-12

description: study sample


title: Group 1 - MC38_precleaned_12

description:
Library name: 2
10x Genomics


title: 200810622-11

description: study sample


title: 200810572-12

description: study sample


title: 200810567-10

description: study sample


title: Rev-nAAC,8w,LV2

city: Shanghai

first: Longming

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center

description:
Library name: D-8W-2
Colunm name in counts_All_Samples.xls:Rev_8w_2

data_processing:
fastp v 0.20.1; HISAT2 v 2.1.0; HTSeq-count v 0.11.2
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2
Read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: xls files include raw counts for each sample

source_name: heart

growth_protocol: The animals were then mated in breeding pairs and kept in a 12-h light and dark circle at room temperature. All neonatal mice subjected to Rev-nAAC, nAAC or sham surgery were co-housed with their mothers and breast fed

extract_protocol:
RNA extraction from mice LV tissues was performed by regular Trizol method.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit® (Vazyme, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Rev-nAAC surgery, Naac surgery or sham surgery was performed

value: heart

tag: treatment

value: Rev-nAAC


title: Rev-nAAC,8w,LV1

description:
Library name: D-8W-1
Colunm name in counts_All_Samples.xls:Rev_8w_1


title: Rev-nAAC,8w,LV5

description:
Library name: D-8W-5
Colunm name in counts_All_Samples.xls:Rev_8w_5


title: Rev-nAAC,8w,LV4

description:
Library name: D-8W-4
Colunm name in counts_All_Samples.xls:Rev_8w_4


title: Rev-nAAC,8w,LV3

description:
Library name: D-8W-3
Colunm name in counts_All_Samples.xls:Rev_8w_3


title: 200810562-09

description: study sample


title: 200810514-10

description: study sample


title: 200810518-09

description: study sample


title: Rev-nAAC,6w,LV4

description:
Library name: D-6W-4
Colunm name in counts_All_Samples.xls:Rev_6w_4


title: 200810503-10

description: study sample


title: Rev-nAAC,6w,LV5

description:
Library name: D-6W-5
Colunm name in counts_All_Samples.xls:Rev_6w_5


title: Group 3 - MC38 + NIH3T3 Aebp1 KO_precleaned_15

description:
Library name: 5
10x Genomics


title: Rev-nAAC,6w,LV3

description:
Library name: D-6W-3
Colunm name in counts_All_Samples.xls:Rev_6w_3


title: 200810443-11

description: study sample


title: 200810493-11

description: study sample


title: 200810501-10

description: study sample


title: 200810498-10

description: study sample


title: 200810475-09

description: study sample


title: Rev-nAAC,6w,LV2

description:
Library name: D-6W-2
Colunm name in counts_All_Samples.xls:Rev_6w_2


title: Rev-nAAC,4w,LV5

description:
Library name: D-4W-5
Colunm name in counts_All_Samples.xls:Rev_4w_5


title: 200810460-10

description: study sample


title: Rev-nAAC,6w,LV1

description:
Library name: D-6W-1
Colunm name in counts_All_Samples.xls:Rev_6w_1


title: Rev-nAAC,4w,LV2

description:
Library name: D-4W-2
Colunm name in counts_All_Samples.xls:Rev_4w_2


title: nAAC,8w,LV5

description:
Library name: B-8W-5
Colunm name in counts_All_Samples.xls:nAAC_8w_5

value: nAAC


title: Rev-nAAC,4w,LV4

description:
Library name: D-4W-4
Colunm name in counts_All_Samples.xls:Rev_4w_4


title: 200810428-10

description: study sample


title: Rev-nAAC,4w,LV3

description:
Library name: D-4W-3
Colunm name in counts_All_Samples.xls:Rev_4w_3


title: Rev-nAAC,4w,LV1

description:
Library name: D-4W-1
Colunm name in counts_All_Samples.xls:Rev_4w_1


title: 200810399-09

description: study sample


title: 200810321-10

description: study sample


title: nAAC,8w,LV2

description:
Library name: B-8W-2
Colunm name in counts_All_Samples.xls:nAAC_8w_2


title: 200810406-10

description: study sample


title: 200810308-13

description: study sample


title: nAAC,8w,LV3

description:
Library name: B-8W-3
Colunm name in counts_All_Samples.xls:nAAC_8w_3


title: 200810329-10

description: study sample


title: nAAC,6w,LV3

description:
Library name: B-6W-3
Colunm name in counts_All_Samples.xls:nAAC_6w_3


title: nAAC,6w,LV4

description:
Library name: B-6W-4
Colunm name in counts_All_Samples.xls:nAAC_6w_4


title: 200810295-11

description: study sample


title: 200810416-11

description: study sample


title: nAAC,8w,LV1

description:
Library name: B-8W-1
Colunm name in counts_All_Samples.xls:nAAC_8w_1


title: nAAC,6w,LV5

description:
Library name: B-6W-5
Colunm name in counts_All_Samples.xls:nAAC_6w_5


title: 200810434-10

description: study sample


title: nAAC,8w,LV4

description:
Library name: B-8W-4
Colunm name in counts_All_Samples.xls:nAAC_8w_4


title: nAAC,6w,LV2

description:
Library name: B-6W-2
Colunm name in counts_All_Samples.xls:nAAC_6w_2


title: nAAC,6w,LV1

description:
Library name: B-6W-1
Colunm name in counts_All_Samples.xls:nAAC_6w_1


title: 200810294-13

description: study sample


title: nAAC,4w,LV3

description:
Library name: B-4W-3
Colunm name in counts_All_Samples.xls:nAAC_4w_3


title: nAAC,4w,LV2

description:
Library name: B-4W-2
Colunm name in counts_All_Samples.xls:nAAC_4w_2


title: 200810284-12

description: study sample


title: 200810252-12

description: study sample


title: 201104275-07

description: study sample


title: nAAC,4w,LV4

description:
Library name: B-4W-4
Colunm name in counts_All_Samples.xls:nAAC_4w_4


title: 201104267-08

description: study sample


title: 200810270-11

description: study sample


title: sham,8w,LV4

description:
Library name: S-8W-4
Colunm name in counts_All_Samples.xls:Sham_8w_4

value: sham


title: nAAC,4w,LV5

description:
Library name: B-4W-5
Colunm name in counts_All_Samples.xls:nAAC_4w_5

value: WT


title: 201104054-05

description: study sample


title: nAAC,4w,LV1

description:
Library name: B-4W-1
Colunm name in counts_All_Samples.xls:nAAC_4w_1


title: 201104187-06

description: study sample


title: 201104180-05

description: study sample


title: sham,6w,LV5

description:
Library name: S-6W-5
Colunm name in counts_All_Samples.xls:Sham_6w_5


title: 201104184-05

description: study sample


title: sham,8w,LV2

description:
Library name: S-8W-2
Colunm name in counts_All_Samples.xls:Sham_8w_2


title: 201104172-07

description: study sample


title: sham,8w,LV5

description:
Library name: S-8W-5
Colunm name in counts_All_Samples.xls:Sham_8w_5


title: sham,8w,LV1

description:
Library name: S-8W-1
Colunm name in counts_All_Samples.xls:Sham_8w_1


title: 201104019-05

description: study sample


title: 201104125-06

description: study sample


title: sham,8w,LV3

description:
Library name: S-8W-3
Colunm name in counts_All_Samples.xls:Sham_8w_3


title: sham,6w,LV4

description:
Library name: S-6W-4
Colunm name in counts_All_Samples.xls:Sham_6w_4


title: sham,6w,LV3

description:
Library name: S-6W-3
Colunm name in counts_All_Samples.xls:Sham_6w_3


title: 201103998-06

description: study sample


title: 201103993-04

description: study sample


title: 201103970-03

description: study sample


title: sham,6w,LV1

description:
Library name: S-6W-1
Colunm name in counts_All_Samples.xls:Sham_6w_1


title: sham,6w,LV2

description:
Library name: S-6W-2
Colunm name in counts_All_Samples.xls:Sham_6w_2


title: 201103966-05

description: study sample


title: 201103964-06

description: study sample


title: sham,4w,LV4

description:
Library name: S-4W-4
Colunm name in counts_All_Samples.xls:Sham_4w_4


title: 201011548-03

description: study sample


title: sham,4w,LV3

description:
Library name: S-4W-3
Colunm name in counts_All_Samples.xls:Sham_4w_3


title: 201011535-05

description: study sample


title: sham,4w,LV5

description:
Library name: S-4W-5
Colunm name in counts_All_Samples.xls:Sham_4w_5


title: sham,4w,LV2

description:
Library name: S-4W-2
Colunm name in counts_All_Samples.xls:Sham_4w_2


title: 201011512-06

description: study sample


title: 200900630-12

description: study sample


title: 201007752-09

description: study sample


title: CT-2

city: Guangzhou

first: Yan

last: Du

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

description: Library name: Sample2

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

source_name: ovary

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using DNA 1000 assay Kit following manufacturer's protocols

value: ovary


title: 200900639-12

description: study sample


title: ZnSO4+ISCK03-3

description: Library name: Sample6


title: 200900626-10

description: study sample


title: 201007423-03

description: study sample


title: 200900625-10

description: study sample


title: sham,4w,LV1

last: Huang

description:
Library name: S-4W-1
Colunm name in counts_All_Samples.xls:Sham_4w_1


title: CT-3

description: Library name: Sample3


title: ZnSO4+ISCK03-2

description: Library name: Sample5


title: ZnSO4+ISCK03-1

description: Library name: Sample4


title: CT-1

description: Library name: Sample1


title: 200900624-14

description: study sample


title: 200900607-10

description: study sample


title: CD4+T cells under Th1 condition for 72h_biol rep 3

first: hu

last: lu

state: State

address: fu kang lu

institute: TMU

description: Library name: T3

data_processing:
Raw data quality control and adapter trimming were performed using fastp to remove adapter-containing reads, poly-N reads and low-quality reads. Q20, Q30 and GC content were calculated.
Trimmed clean reads were aligned to the mm10 reference genome using HISAT2 v2.0.5 with splice-aware alignment (genome index built using gene model annotations)
Gene-level read counts were quantified using featureCounts v1.5.0-p3 with mm10 gene annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: CD4+ T cells

extract_protocol:
Total RNA were extracted using Trizol, RNA integrity was verified using the Agilent Bioanalyzer 2100.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: CD4+ T cells

value: under Th1 condition for 72h


title: CD4+T cells under Th1 condition for 72h with ALX-5407 treatment_biol rep 2

description: Library name: ALX-54072


title: CD4+T cells under Th1 condition for 72h with ALX-5407 treatment_biol rep 1

description: Library name: ALX-54071


title: 200900591-12

description: study sample


title: CD4+T cells under Th1 condition for 72h with ALX-5407 treatment_biol rep 3

description: Library name: ALX-54073


title: 201011430-06

description: study sample


title: 200900599-10

description: study sample


title: CD4+T cells under Th1 condition for 72h_biol rep 2

description: Library name: T2


title: 200811187-11

description: study sample


title: CD4+T cells under Th1 condition for 72h_biol rep 1

description: Library name: T1


title: 200811195-09

description: study sample


title: Tumor, MSA-2 treatment

city: Hangzhou

first: Fanchao

last: Meng

address: 79 Qingchun Road

department: NHC Key Laboratory of Combined Multi-Organ Transplantation

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

description: Library name: Treated

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. After mapping with Cell Ranger (v7.0.0) on the mouse reference, downstream single-cell analyses were further performed using Seurat (v4.3.0).
Assembly: mm10
Supplementary files format and content: matrix.mtx
Supplementary files format and content: features.tsv
Supplementary files format and content: barcodes.tsv

source_name: Tumor

extract_protocol:
The cell suspension was prepared according to general protocols and loaded into Chromium microfluidic chips with 3’ (v3.1) chemistry and barcoded with a 10X Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
The sequencing libraries were constructed using a Chromium Single Cell 3’ (v3.1) reagent kit (10X Genomics) (Novogene). Illumina NovaSeq 6000 PE150 was used for sequencing following the manufacturer’s instructions.

value: Tumor

value: tumor cells

value: MSA-2 treatment


title: Tumor, Untreated, negative control

description: Library name: Control

value: Untreated, negative control


title: 200811100-09

description: study sample


title: 200811037-11

description: study sample


title: mESC, Naïve, cytoplasm, PANDORA-seq, rep4

description: Library name: mESC-naive-cyto_PANDORAseq_4

data_processing:
The raw reads were trimmed by performing SPORTS1.1.2 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Naive ES cells

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Naive ES cells

tag: fraction

value: Cytoplasm

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before small RNA library construction.


title: 200811006-10

description: study sample


title: 200811016-09

description: study sample


title: mESC, Naïve, cytoplasm, PANDORA-seq, rep1

description: Library name: mESC-naive-cyto_PANDORAseq_1


title: 200811012-11

description: study sample


title: 200810999-09

description: study sample


title: mESC, Naïve, cytoplasm, PANDORA-seq, rep2

description: Library name: mESC-naive-cyto_PANDORAseq_2


title: mESC, Naïve, cytoplasm, PANDORA-seq, rep3

description: Library name: mESC-naive-cyto_PANDORAseq_3


title: mESC, Naïve, pbody, PANDORA-seq, rep3

description: Library name: mESC-naive-pbody_PANDORAseq_3

value: Pbody


title: 200810998-13

description: study sample

value: Blood


title: 200810992-10

description: study sample


title: mESC, Naïve, pbody, PANDORA-seq, rep2

description: Library name: mESC-naive-pbody_PANDORAseq_2


title: mESC, Naïve, pbody, PANDORA-seq, rep1

description: Library name: mESC-naive-pbody_PANDORAseq_1


title: 200810962-11

description: study sample


title: 200811109-08

description: study sample


title: 200810952-10

description: study sample


title: mESC, primed, cytoplasm, PANDORA-seq, rep4

description: Library name: mESC-primed-cyto_PANDORAseq_4

value: Primed ES cells


title: mESC, primed, cytoplasm, PANDORA-seq, rep3

description: Library name: mESC-primed-cyto_PANDORAseq_3


title: 200810983-07

description: study sample


title: mESC, primed, cytoplasm, PANDORA-seq, rep1

description: Library name: mESC-primed-cyto_PANDORAseq_1


title: 200810921-09

description: study sample


title: mESC, primed, cytoplasm, PANDORA-seq, rep2

description: Library name: mESC-primed-cyto_PANDORAseq_2


title: mESC, primed, pbody, PANDORA-seq, rep3

description: Library name: mESC-primed-pbody_PANDORAseq_3


title: mESC, primed, pbody, PANDORA-seq, rep2

description: Library name: mESC-primed-pbody_PANDORAseq_2


title: 200810888-09

description: study sample


title: mESC, primed, pbody, PANDORA-seq, rep4

description: Library name: mESC-primed-pbody_PANDORAseq_4


title: mESC, Naïve, pbody, PANDORA-seq, rep4

description: Library name: mESC-naive-pbody_PANDORAseq_4


title: 200810867-11

description: study sample


title: 200810789-09

description: study sample


title: mFibroblast, cytoplasm, PANDORA-seq, rep4

description: Library name: mFibroblast-cyto_PANDORAseq_4

source_name: Fibroblast

value: Fibroblast


title: mESC, primed, pbody, PANDORA-seq, rep1

description: Library name: mESC-primed-pbody_PANDORAseq_1

source_name: Primed ES cells


title: mFibroblast, cytoplasm, PANDORA-seq, rep3

description: Library name: mFibroblast-cyto_PANDORAseq_3