title: NCI-H69 cells, P300 knockdown, biological replicate 3

city: suzhou

first: Jiahao

address: Address: 16 Baita West Road, Gusu District, Suzhou

institute: SUZHOU MUNICIPAL HOSPITAL

description:
Library name: si_P300_3
Single-end 50 bp RNA-seq; column name in gene_expression.xls: si_P300_3

data_processing:
Raw reads were filtered to remove adapter-containing reads, low-quality reads, and reads with excessive unknown base content to generate clean reads.
Clean reads were aligned to the human reference genome GCF_000001405.39_GRCh38.p13 using HISAT.
Clean reads were aligned to the reference gene set using Bowtie2, and gene-level expression values were generated in gene_expression.xls.
Differential expression analysis was performed for si_CSNK2B versus negative control and si_P300 versus negative control.
Sample names in the BGI short report were corrected for this GEO metadata as instructed by the submitter: si_IRF1 corresponds to si_CSNK2B, and si_RBBP4 corresponds to si_P300.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: gene_expression.xls: gene-level expression file for all nine samples included in this submission.

growth_protocol: NCI-H69 small cell lung cancer cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2. Cells were routinely tested negative for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from NCI-H69 cells after siRNA transfection. RNA quantity and quality were assessed before library construction. RNA samples were submitted for bulk RNA-seq library preparation and sequencing by BGI.
Bulk RNA-seq libraries were prepared by BGI from RNA samples and sequenced as single-end 50 bp reads on the BGISEQ platform.

treatment_protocol: NCI-H69 cells were transfected with negative control siRNA, CSNK2B-targeting siRNA, or P300-targeting siRNA. Total RNA was harvested 48 hours after transfection.

value: small cell lung cancer cell

value: P300 siRNA; RNA harvested 48 h after transfection


title: NCI-H69 cells, P300 knockdown, biological replicate 2

status: Public on Jul 04 2026

type: SRA

last: Guo

country: China

description:
Library name: si_P300_2
Single-end 50 bp RNA-seq; column name in gene_expression.xls: si_P300_2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: mvi_no5

city: HANGZHOU

first: Xin

last: Hu

address: YUHANGTANGROAD 866

institute: Zhejiang university

data_processing:
Raw reads were treated with Trimmomatictools(V0.36) to remove adapters. Following reads quality con- trol:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using theFastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human- reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively. CIRI2 detectsthe paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment withBWA-MEM and combines with systematic filtering steps to remove potential false positives.CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
If a circRNA can be detected by both methods, it will be consided as an identified circRNA. The DEseq/DESeq2/edgeR/DEGse package in Bioconductor was used to determine differently expressed circRNAs, according to the criteria of |log2 (fold change) | >1 and p-value≤005
Assembly: hg38

source_name: liver - hepatocellular carcinoma

growth_protocol: The HCC tissues of the patients were preserved in -80 environment after resection

extract_protocol:
none
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufac- turer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to in- structions ofNEBNext® UltraTM RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp

tag: tissue

value: liver - hepatocellular carcinoma


title: Tex1,Mezi,H3K4me1 (ChIP)

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

country: USA

institute: Bristol Myers Squibb

description: Library name: Tex1-480_H3K4me1

library_source: genomic

data_processing:
We used MACS version 3.0.1 to call peaks.
Assembly: GRCh38
Supplementary files format and content: narrowpeak

molecule: genomic DNA

source_name: cell line

extract_protocol:
DNA was extracted and purified using the standard phenol chloroform method, followed by ethanol precipitation.
Library was prepared using an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: T-cell

value: Mezi


title: Kmt2d WT 971 cell cut&run seq Smarcc1

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

description: Library name: CR_kmt2d_SKCM_971_J, Cut_Run

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by Bowtie2
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs1 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: mm10
Supplementary files format and content: peaks files: .narrowPeaks, .broadPeaks
Supplementary files format and content: bigwig files: .bw
Library strategy: CUT&RUN

organism: Mus musculus

source_name: Kmt2d WT 971

growth_protocol: Mouse melanoma cells were grown in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Epicypher cut and run protocol v2.1
Epicypher CUTANA™ CUT&RUN Library Prep Kit

tag: disease state

value: Melanoma

value: Kmt2d WT 971

tag: chip antibody

value: Anti-Smarcc1 CST 11956S


title: NCI-H69 cells, P300 knockdown, biological replicate 1

description:
Library name: si_P300_1
Single-end 50 bp RNA-seq; column name in gene_expression.xls: si_P300_1


title: Kmt2d WT 971 cell cut&run seq KMT2D

description: Library name: CR_kmt2d_SKCM_971_H, Cut_Run

value: Anti-KMT2D Millipore ABE1867


title: mvi_no4


title: Tex3,DMSO,H3K27Ac (ChIP)

description: Library name: Tex3-DMSO_H3K27Ac

value: DMSO


title: NCI-H69 cells, CSNK2B knockdown, biological replicate 3

description:
Library name: si_CSNK2B_3
Single-end 50 bp RNA-seq; column name in gene_expression.xls: si_CSNK2B_3

value: CSNK2B siRNA; RNA harvested 48 h after transfection


title: Kmt2d WT 971 cell cut&run seq Rabbit IgG

description: Library name: CR_kmt2d_SKCM_971_G, IgG

value: Rabbit IgG Abcam ab172730


title: mvi_no3


title: Tex3,Mezi,H3K27Ac (ChIP)

description: Library name: Tex3-480_H3K27Ac


title: NCI-H69 cells, CSNK2B knockdown, biological replicate 2

description:
Library name: si_CSNK2B_2
Single-end 50 bp RNA-seq; column name in gene_expression.xls: si_CSNK2B_2


title: mvi_no2


title: Kmt2d WT 971 cell cut&run seq H3K4me3

description: Library name: CR_kmt2d_SKCM_971_B, Cut_Run

value: H3K4me3 Abcam ab8580


title: Tex2,DMSO,H3K27Ac (ChIP)

description: Library name: Tex2-DMSO_H3K27Ac


title: Kmt2d mutant 493 cell Chipseq H3K4me1

description: Library name: IBM_SKCM_M493_A, ChIP

data_processing:
1. Quality Control by using fastqc and multiqc, then trim the sequences if needed
2. aligning the sequences by BMA
3. filtering the data and remove the duplicates, downsampling
4. calling the peaks by using macs1 for narrow peaks and macs2 for broad peaks
5. generating bigwig files
Assembly: mm10
Supplementary files format and content: .narrowPeaks, .broadPeaks
Supplementary files format and content: bigwig

source_name: Kmt2d Mutant 493

extract_protocol:
Following the protocol on: Terranova, Christopher, et al. "An integrated platform for genome-wide mapping of chromatin states using high-throughput ChIP-sequencing in tumor tissues." Journal of visualized experiments: JoVE 134 (2018).
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

value: Kmt2d Mutant 493

value: H3K4me1 abcam ab8895


title: NCI-H69 cells, CSNK2B knockdown, biological replicate 1

description:
Library name: si_CSNK2B_1
Single-end 50 bp RNA-seq; column name in gene_expression.xls: si_CSNK2B_1


title: Kmt2d mutant 493 cell cut&run seq SOX10 U

description: Library name: CR_kmt2d_SKCM_493_U, Cut_Run

value: Anti-SOX10 CST 69661


title: mvi_no1


title: Tex2,Mezi,H3K27Ac (ChIP)

description: Library name: Tex2-480_H3K27Ac


title: Kmt2d mutant 493 cell cut&run seq SOX10 T

description: Library name: CR_kmt2d_SKCM_493_T, Cut_Run

value: Anti-SOX10 Bethyl A305-799A-T


title: NCI-H69 cells, negative control siRNA, biological replicate 3

description:
Library name: NC3
Single-end 50 bp RNA-seq; column name in gene_expression.xls: NC3

value: small cell lung cancer cell

value: negative control siRNA; RNA harvested 48 h after transfection


title: siRNA-4

data_processing:
Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Paired-end reads were aligned to the humam reference genome hg38 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(foldchange)| > 1 using theDEseq/DESeq2/edgeR/DEGseq software. Finally, a hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values and counts for each Sample/xlsx

source_name: liver

growth_protocol: HCCLM3cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (BI, Israel), which was composed of 10% fetal bovine serum (FBS) (BI, Israel) and 1% penicillin-streptomycin (Gibco, USA). The cells were maintained at 37°C in a humidified incubator with 5% CO2

extract_protocol:
NOne
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufac- turer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to in- structions ofNEBNext® UltraTM RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp

treatment_protocol: SiRNA (targeted to circPTK2) was transiently transfected into cells by means of DNA transfection reagent (Polyplus, France) based on the manufacturer’s instructions

value: liver

value: Hepatocellular carcinoma cell

tag: genotype

value: circPTK2 knock down


title: Tex1,DMSO,H3K27Ac (ChIP)

description: Library name: Tex1-DMSO_H3K27Ac

value: T-cell


title: NCI-H69 cells, negative control siRNA, biological replicate 2

description:
Library name: NC2
Single-end 50 bp RNA-seq; column name in gene_expression.xls: NC2


title: Kmt2d mutant 493 cell cut&run seq TFAP2B

description: Library name: CR_kmt2d_SKCM_493_S, Cut_Run

value: Melanoma

value: Anti-TFAP2B Proteintech 13183-1-AP


title: siRNA-3


title: Tex1,Mezi,H3K27Ac (ChIP)

description: Library name: Tex1-480_H3K27Ac

value: Mezi


title: NCI-H69 cells, negative control siRNA, biological replicate 1

description:
Library name: NC1
Single-end 50 bp RNA-seq; column name in gene_expression.xls: NC1


title: Kmt2d mutant 493 cell cut&run seq TFAP2A

description: Library name: CR_kmt2d_SKCM_493_R, Cut_Run

value: Anti-TFAP2A Proteintech 13019-3-AP


title: siRNA-2


title: Tex3,Mezi,Ikaros (ChIP)

description: Library name: Tex3-480_Ikaros

value: DMSO


title: Kmt2d mutant 493 cell cut&run seq UTX

description: Library name: CR_kmt2d_SKCM_493_P, Cut_Run

value: Anti-UTX Millipore ABE1865


title: ULA_NP_3

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

description:
Library name: ULA_NP_3
sgNTC control ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with PBS vehicle; biological replicate 3

data_processing:
Adapter and low-quality base trimming of paired-end reads with Trimmomatic (ILLUMINACLIP with Novogene adapters; LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Trimmed read pairs were aligned to the mouse reference genome (mm10) with HISAT2.
Alignments were converted to BAM, coordinate-sorted, and indexed with SAMtools.
Gene-level fragment quantification with featureCounts (Subread v2.1.1) in paired-end mode (-p) using the mm10 gene annotation (genes.gtf).
Count matrices were analyzed in R: differential expression with DESeq2 (variance-stabilizing transformation for PCA/visualization) and pathway enrichment with clusterProfiler (Hallmark, Reactome, GO Biological Process).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited featureCounts output, one .txt file per sample. Each file lists gene-level fields (Geneid [Ensembl ENSMUSG], Chr, Start, End, Strand, Length) followed by a column of raw fragment counts for that sample.

molecule: polyA RNA

source_name: ovary

growth_protocol: ID8 p53-/- (Ifngr1-KO or sgNTC) ovarian cancer cells were seeded at 3.0x10^5 cells/well into 6-well regular (adherent) or ultra-low attachment plates and cultured for 48 hours.

extract_protocol:
For ultra-low attachment samples, dead cells were removed prior to extraction. Total RNA was isolated using the Direct-zol RNA Miniprep kit with TriReagent following the manufacturer's protocol.
Poly-A mRNA was purified using poly-T oligo-attached magnetic beads, fragmented, and reverse transcribed to cDNA, which was end-repaired, adapter-ligated, amplified, and indexed to generate final libraries.

treatment_protocol: Twenty-four hours after seeding, wells received recombinant mouse IFN-gamma (100 ng/ml) or an equivalent volume of vehicle (1x PBS). Cells were harvested 24 hours after treatment (48 hours after seeding).

value: ovary

value: ovarian cancer cell

value: sgNTC (non-targeting control)

tag: culture condition

value: ultra-low attachment

value: PBS (vehicle)


title: Tex3,DMSO,Ikaros (ChIP)

description: Library name: Tex3-DMSO_Ikaros


title: siRNA-1


title: NC-4

value: WT


title: Tex2,DMSO,Ikaros (ChIP)

description: Library name: Tex2-DMSO_Ikaros


title: Kmt2d mutant 493 cell cut&run seq Menin

description: Library name: CR_kmt2d_SKCM_493_O, Cut_Run

value: Kmt2d Mutant 493

value: Anti-Menin Epicypher 13-2021


title: ULA_NP_2

description:
Library name: ULA_NP_2
sgNTC control ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with PBS vehicle; biological replicate 2


title: Kmt2d mutant 493 cell cut&run seq BRD9

description: Library name: CR_kmt2d_SKCM_493_N, Cut_Run

value: Anti-BRD9 Bethyl A303-781A-T


title: ULA_NP_1

description:
Library name: ULA_NP_1
sgNTC control ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with PBS vehicle; biological replicate 1


title: Tex2,Mezi,Ikaros (ChIP)

description: Library name: Tex2-480_Ikaros


title: NC-3

value: liver

value: Hepatocellular carcinoma cell


title: Kmt2d mutant 493 cell cut&run seq PBRM1

description: Library name: CR_kmt2d_SKCM_493_M, Cut_Run

value: Melanoma

value: Anti-PBRM1 Bethyl A301-591A-T


title: ULA_NI_3

description:
Library name: ULA_NI_3
sgNTC control ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with IFN-gamma; biological replicate 3

value: IFN-gamma (100 ng/ml)


title: NC-2


title: Tex1,DMSO,Ikaros (ChIP)

description: Library name: Tex1-DMSO_Ikaros

value: T-cell


title: Kmt2d mutant 493 cell cut&run seq Arid2

description: Library name: CR_kmt2d_SKCM_493_L, Cut_Run

value: Anti-Arid2 Bethyl A302-230A-T


title: NC-1


title: ULA_NI_2

description:
Library name: ULA_NI_2
sgNTC control ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with IFN-gamma; biological replicate 2


title: ULA_NI_1

description:
Library name: ULA_NI_1
sgNTC control ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with IFN-gamma; biological replicate 1


title: Tex1,Mezi,Ikaros (ChIP)

description: Library name: Tex1-480_Ikaros

value: Mezi


title: Kmt2d mutant 493 cell cut&run seq Arid1a

description: Library name: CR_kmt2d_SKCM_493_K, Cut_Run

value: Anti-Arid1a Abcam ab182560


title: HEK 293T cells SIDT2 shRNA-D-4

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

description: Library name: KDD-4

data_processing:
The reads were trimmed for adapters and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp (Chen et al. 2018). The count tables were generated by aligning the trimmed reads to the human transcriptome (Ensembl version 113) using kallisto (Bray et al. 2016). The transcript counts were converted to gene counts using tximport (Soneson, Love, and Robinson 2015).
Assembly: Ensembl version 113)
Supplementary files format and content: CSV of counts

source_name: HEK 293T

growth_protocol: HEK 293T cells were cultured in Dulbecco’s Modified Eagle Medium containing 4500 mg/L glucose and 110 mg/L pyruvate (Thermo Fisher 11995-065) supplemented with 10% heat-inactivated FBS and 2 mM glutamine at 37 °C with 5% CO₂.

extract_protocol:
RNA was extracted using TRIzol (for cells, Invitrogen 15596018) and the Direct-zol RNA Miniprep kit (Zymo Research R2050)
Kapa mRNA -PolyA Selection

treatment_protocol: HEK293T cells were transduced with SIDT2 shRNA lentivirus (Cellecta CPCP-K2A packaging system) in the presence of 4 μg/mL polybrene to generate SIDT2 knockdown cells. Cells were harvested 72 h after transduction.

value: HEK 293T


title: Tact3,DMSO,H3K4me3 (ChIP)

description: Library name: Tact3-DMSO_H3K4me3

value: DMSO


title: HEK 293T cells SIDT2 shRNA-B-4

description: Library name: KDB-4


title: Kmt2d mutant 493 cell cut&run seq Smarcc1

description: Library name: CR_kmt2d_SKCM_493_J, Cut_Run

value: Anti-Smarcc1 CST 11956S


title: ULA_C2P_3

description:
Library name: ULA_C2P_3
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with PBS vehicle; biological replicate 3

value: ovary

value: ovarian cancer cell

value: ultra-low attachment

value: PBS (vehicle)


title: Tact2,DMSO,H3K4me3 (ChIP)

description: Library name: Tact2-DMSO_H3K4me3


title: ULA_C2P_2

description:
Library name: ULA_C2P_2
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with PBS vehicle; biological replicate 2


title: HEK 293T cells scramble shRNA-4

description: Library name: SCR-4


title: Tact1,DMSO,H3K4me3 (ChIP)

description: Library name: Tact1-DMSO_H3K4me3


title: ULA_C2P_1

description:
Library name: ULA_C2P_1
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with PBS vehicle; biological replicate 1


title: Kmt2d mutant 493 cell cut&run seq Rabbit IgG

description: Library name: CR_kmt2d_SKCM_493_G, IgG

value: Kmt2d Mutant 493

value: Rabbit IgG Abcam ab172730


title: Kmt2d mutant 493 cell cut&run seq H3K4me3

description: Library name: CR_kmt2d_SKCM_493_B, Cut_Run

value: H3K4me3 Abcam ab8580


title: HEK 293T cells SIDT2 shRNA-D-3

description: Library name: KDD-3


title: Tact3,DMSO,H3K4me1 (ChIP)

description: Library name: Tact3-DMSO_H3K4me1


title: EpH4-AS_3D_PM_treatment_2

city: Linz

first: Tamara

last: Lang

address: Krankenhausstraße 5

department: Pathophysiology

country: Austria

institute: Johannes Kepler Universität

description:
Library name: S8
Column name in "Counts_all.csv": S8

data_processing:
CLC Genomics Workbench v 24.0.2
Reads were trimmed for quality (Phred < 13), adapter sequences, polyG tails and reads with > 2 ambiguous bases using CLC Genomics Workbench.
Trimmed reads were mapped to GRCm39 using CLC Genomics Workbench. (Parameters: Mismatch Cost: 2; Insertion Cost: 3; Deletion Cost: 3; Length Fraction: 0.8; Similaryity Fraction: 0.8; Maximum number of hits for a read: 10; Auto-detect paired distances)
Read count extraction and (TPM, RPKM) normalization were performed using CLC Genomics Workbench.
Assembly: GRCm39
Supplementary files format and content: Comma-Separated-Values-File. Includes gene names and properties. Describes the expression in each sample as raw total counts and RPKM-normalized values.
Supplementary files format and content: Comma-Separated-Values-File. Includes gene names and identifiers. Describes the raw count and (RPKM-) normalized expression of all genes in the sample.

source_name: epithelial

extract_protocol:
Total RNA was extracted using the ReliaPrep RNA Miniprep System according to the manufacturer's protocol. 750 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-Seq were prepared using the Illumina Stranded mRNA Prep, Ligation Kit following the manufacturer's protocol.

value: epithelial

value: Epithelial cell of the mammary gland

value: AS-transformed

tag: batch


title: HEK 293T cells SIDT2 shRNA-B-3

description: Library name: KDB-3


title: Tact2,DMSO,H3K4me1 (ChIP)

description: Library name: Tact2-DMSO_H3K4me1

value: T-cell


title: ULA_C2I_3

description:
Library name: ULA_C2I_3
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with IFN-gamma; biological replicate 3

value: IFN-gamma (100 ng/ml)


title: EpH4-AS_3D_PM_treatment_1

description:
Library name: S7
Column name in "Counts_all.csv": S7


title: Tact1,DMSO,H3K4me1 (ChIP)

description: Library name: Tact1-DMSO_H3K4me1


title: ULA_C2I_1

description:
Library name: ULA_C2I_1
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with IFN-gamma; biological replicate 1


title: ULA_C2I_2

description:
Library name: ULA_C2I_2
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under ultra-low attachment conditions and treated with IFN-gamma; biological replicate 2


title: EpH4-AS_3D_Control_2

description:
Library name: S6
Column name in "Counts_all.csv": S6

value: Control


title: HEK 293T cells SIDT2 shRNA-D-2

description: Library name: KDD-2


title: Tact3,DMSO,H3K27Ac (ChIP)

description: Library name: Tact3-DMSO_H3K27Ac


title: HEK 293T cells scramble shRNA-3

description: Library name: SCR-3


title: HEK 293T cells SIDT2 shRNA-B-2

description: Library name: KDB-2


title: Reg_NP_3

description:
Library name: Reg_NP_3
sgNTC control ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with PBS vehicle; biological replicate 3

value: sgNTC (non-targeting control)

value: adherent


title: Tact2,DMSO,H3K27Ac (ChIP)

description: Library name: Tact2-DMSO_H3K27Ac

value: DMSO


title: EpH4-AS_3D_Control_1

description:
Library name: S5
Column name in "Counts_all.csv": S5


title: EpH4_3D_PM_treatment_2

description:
Library name: S4
Column name in "Counts_all.csv": S4

value: WT


title: HEK 293T cells scramble shRNA-2

description: Library name: SCR-2

value: HEK 293T


title: Tact1,DMSO,H3K27Ac (ChIP)

description: Library name: Tact1-DMSO_H3K27Ac


title: Reg_NP_2

description:
Library name: Reg_NP_2
sgNTC control ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with PBS vehicle; biological replicate 2

value: ovary

value: ovarian cancer cell


title: Reg_NP_1

description:
Library name: Reg_NP_1
sgNTC control ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with PBS vehicle; biological replicate 1

value: PBS (vehicle)


title: HEK 293T cells SIDT2 shRNA-D-1

description: Library name: KDD-1


title: EpH4_3D_PM_treatment_1

description:
Library name: S3
Column name in "Counts_all.csv": S3


title: Tact3,DMSO,Ikaros (ChIP)

description: Library name: Tact3-DMSO_Ikaros


title: EpH4_3D_Control_2

description:
Library name: S2
Column name in "Counts_all.csv": S2


title: HEK 293T cells SIDT2 shRNA-B-1

description: Library name: KDB-1


title: Reg_NI_3

description:
Library name: Reg_NI_3
sgNTC control ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with IFN-gamma; biological replicate 3


title: Tact2,DMSO,Ikaros (ChIP)

description: Library name: Tact2-DMSO_Ikaros


title: Reg_NI_2

description:
Library name: Reg_NI_2
sgNTC control ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with IFN-gamma; biological replicate 2


title: EpH4_3D_Control_1

description:
Library name: S1
Column name in "Counts_all.csv": S1


title: HEK 293T cells scramble shRNA-1

description: Library name: SCR-1


title: Tact1,DMSO,Ikaros (ChIP)

description: Library name: Tact1-DMSO_Ikaros


title: INPUT

description: Library name: Pooled_Input


title: Sham-treated diabetic foot rat plasma sEVs rep3

city: Nanning

first: Sijie

last: Yang

state: Guangxi, P. R.

address: No.6, Taoyuan Road

department: Department of Plastic and Aesthetic Surgery

institute: The People’s Hospital of Guangxi Zhuang Autonomous Region

description:
Library name: S3
Small RNA sequencing of plasma-derived sEVs from a sham-operated diabetic foot Sprague-Dawley rat, replicate 3

data_processing:
Raw sequencing reads were processed to remove adapter sequences, low-quality reads, reads containing ambiguous bases, and reads shorter than 18 nt or longer than 30 nt.
Clean reads were collapsed into unique sequences and length distribution was assessed.
Clean small RNA reads were mapped to the Rattus norvegicus reference genome using Bowtie, allowing limited mismatches according to the small RNA alignment criteria.
Known miRNAs were identified by comparison with mature and precursor miRNA sequences in miRBase. Unannotated reads were further analyzed to predict potential novel miRNAs.
miRNA expression levels were quantified and normalized as TPM. Differentially expressed miRNAs between the tibial transverse transport group and sham-operated group were identified based on normalized expression values.
Assembly: Rnor_6.0
Supplementary files format and content: Excel workbook containing expressed miRNA profiles and normalized expression values for each sample.

organism: Rattus norvegicus

source_name: peripheral blood plasma

growth_protocol: Sprague-Dawley rats were used to establish a diabetic foot model. All rats were maintained under standard specific-pathogen-free conditions with free access to food and water. Peripheral blood samples were collected after the indicated treatment, and plasma was isolated for small extracellular vesicle preparation.

extract_protocol:
Plasma-derived small extracellular vesicles were isolated from peripheral blood plasma. Total RNA was extracted from plasma sEVs using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and quality were assessed before small RNA library construction.
Small RNA libraries were constructed using total RNA extracted from plasma-derived sEVs. Briefly, small RNAs were ligated with 3′ and 5′ adapters, reverse-transcribed into cDNA, amplified by PCR, and size-selected to enrich small RNA fragments corresponding to miRNAs. The prepared libraries were subjected to high-throughput sequencing on an Illumina platform.

treatment_protocol: Diabetic foot rats were assigned to the tibial transverse transport group or the sham-operated group. Rats in the tibial transverse transport group received tibial transverse transport treatment, whereas rats in the sham-operated group underwent the same surgical exposure without tibial transport. Plasma-derived small extracellular vesicles were isolated from peripheral blood samples for miRNA sequencing.

value: peripheral blood plasma

value: wild type

value: sham surgery


title: Reg_NI_1

description:
Library name: Reg_NI_1
sgNTC control ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with IFN-gamma; biological replicate 1


title: S14772Nr12_A549_siGOLM1-2_4

city: Helsinki

first: Meghana

last: Nagaraj

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institute for Medical Research

description:
Library name: siGOLM1-2_4
A549 cells transfected with siGOLM1-2, biological replicate 4

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v2.20). Adapter sequences were trimmed using Skewer (v0.2.2).
Trimmed reads were aligned to the hg19 human reference genome using STAR (v2.7.3).
Gene-level read counts were generated and differential gene expression analysis was performed using DESeq2 (v1.24.0).
KEGG pathway enrichment analysis was performed using clusterProfiler. Reactome pathway enrichment analysis was performed separately by the authors.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files containing raw gene counts, normalized gene counts, differential expression analysis results, and significantly differentially expressed genes generated using DESeq2.

growth_protocol: A549 human lung adenocarcinoma cells (ATCC CCL-185) were cultured in F-12K Nutrient Mixture Kaighn's Modification Medium (Gibco) supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated from A549 cells 72 h after transfection and submitted to CeGaT GmbH (Tübingen, Germany) for quality assessment, library preparation and RNA sequencing.
RNA libraries were prepared from 200 ng total RNA using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Libraries were sequenced on the Illumina NovaSeq X Plus platform using paired-end 2 × 101 bp sequencing.

treatment_protocol: A549 cells were reverse transfected with 50 nM non-targeting control siRNA, siGOLM1-1 or siGOLM1-2 using Lipofectamine RNAiMAX (Invitrogen). Cells were harvested 72 h after transfection for RNA extraction.

value: Lung adenocarcinoma cells

value: GOLM1 KD with siRNA 2


title: Reg_C2P_3

description:
Library name: Reg_C2P_3
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with PBS vehicle; biological replicate 3


title: Sham-treated diabetic foot rat plasma sEVs rep2

description:
Library name: S2
Small RNA sequencing of plasma-derived sEVs from a sham-operated diabetic foot Sprague-Dawley rat, replicate 2


title: S14772Nr11_A549_siGOLM1-2_3

description:
Library name: siGOLM1-2_3
A549 cells transfected with siGOLM1-2, biological replicate 3


title: MM12 Tact Mezi (scATACseq)

description: Library name: MM12_act_Mezi

library_source: genomic single cell

data_processing:
Cellranger was used to processes raw sequencing data to align reads, generate gene-cell matrices.
Assembly: GRCh38
Supplementary files format and content: bed, fragments file

extract_protocol:
MM PBMCs were thawed, treated with either DMSO or 1 nM Mezigdomide for 1 hour, and stimulated with anti-CD3/CD28 Dynabeads for another 3 days followed by library preparation.
Single-nucleus ATAC libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits v1, following the manufacturer’s protocol.

value: Mezi


title: Reg_C2P_2

description:
Library name: Reg_C2P_2
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with PBS vehicle; biological replicate 2


title: S14772Nr10_A549_siGOLM1-2_2

description:
Library name: siGOLM1-2_2
A549 cells transfected with siGOLM1-2, biological replicate 2


title: MM12 Tact DMSO (scATACseq)

description: Library name: MM12_act_DMSO

value: T-cell


title: Sham-treated diabetic foot rat plasma sEVs rep1

description:
Library name: S1
Small RNA sequencing of plasma-derived sEVs from a sham-operated diabetic foot Sprague-Dawley rat, replicate 1


title: Reg_C2P_1

description:
Library name: Reg_C2P_1
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with PBS vehicle; biological replicate 1


title: S14772Nr9_A549_siGOLM1-2_1

description:
Library name: siGOLM1-2_1
A549 cells transfected with siGOLM1-2, biological replicate 1


title: MM11 Tact Mezi (scATACseq)

description: Library name: MM11_act_Mezi


title: TTT-treated diabetic foot rat plasma sEVs rep3

description:
Library name: T3
Small RNA sequencing of plasma-derived sEVs from a TTT-treated diabetic foot Sprague-Dawley rat, replicate 3

value: tibial cortex transverse transport


title: S14772Nr8_A549_siGOLM1-1_4

description:
Library name: siGOLM1-1_4
A549 cells transfected with siGOLM1-1, biological replicate 4

value: GOLM1 KD with siRNA 1


title: Reg_C2I_3

description:
Library name: Reg_C2I_3
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with IFN-gamma; biological replicate 3

value: IFN-gamma (100 ng/ml)


title: TTT-treated diabetic foot rat plasma sEVs rep2

description:
Library name: T2
Small RNA sequencing of plasma-derived sEVs from a TTT-treated diabetic foot Sprague-Dawley rat, replicate 2


title: Reg_C2I_2

description:
Library name: Reg_C2I_2
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with IFN-gamma; biological replicate 2

value: adherent


title: S14772Nr7_A549_siGOLM1-1_3

description:
Library name: siGOLM1-1_3
A549 cells transfected with siGOLM1-1, biological replicate 3


title: MM11 Tact DMSO (scATACseq)

description: Library name: MM11_act_DMSO

value: DMSO


title: TTT-treated diabetic foot rat plasma sEVs rep1

description:
Library name: T1
Small RNA sequencing of plasma-derived sEVs from a TTT-treated diabetic foot Sprague-Dawley rat, replicate 1


title: MM2 Tact Mezi (scATACseq)

description: Library name: MM2_act_Mezi


title: S14772Nr6_A549_siGOLM1-1_2

description:
Library name: siGOLM1-1_2
A549 cells transfected with siGOLM1-1, biological replicate 2


title: Reg_C2I_1

description:
Library name: Reg_C2I_1
Ifngr1-KO ID8 p53-/- ovarian cancer cells cultured under adherent conditions and treated with IFN-gamma; biological replicate 1


title: GM_MR_3

city: BOSTON

first: Shaowen

last: White

address: 181 Longwood Ave, Channing Labs Room 861

department: Medicine

institute: Brigham and Women's Hospital

description: Library name: T_12

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped to the human GRCh38, hg19 genome assembly using STAR v2.7.10a
genes were filtered based on having at least 10 reads in at least 3 samples
DESeq2 v1.48.2 was used to evaluate gene differential expression (DE)
Assembly: GRCh38.p14 (GCF_000001405.40 ), Akata EBV genom (GCA_900004315.1)
Supplementary files format and content: csv files with normalized read counts
MR_Chr38_readcounts.tsv is alignment to human genome Chr38. MR_Akata_readcounts.tsv is alignment to Epstein-Barr virus strain Akata genome. Since it is a viral genome, there are ~83 genes.

source_name: lymphoblastoid cell

growth_protocol: GM12878 cells were maintained in RPMI media with 10% fetal bovine serum (FBS) and antibiotics in humidified chamber with 5% CO2 at 37C. NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunocompromised were originally procured from Jackson Labs, strain #005557, and bred in house at Cornell University, Ithaca under the supervision of Cornell’s animal breeding program. Eight week old, mixed gender NSG were used for the study under the approval of the IACUC committee (protocol #2017-0035). The Center for Animal Resources and Education (CARE) staff, a team of veterinarians and technicians, monitored animal health daily for abnormal behavior, body condition, and tumor burden. Animals were housed in microisolator cages, no more than five mice per cage, on a 12 h light/12 h dark light cycle, given water ad libitum, and food was given according to experimental design.

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads
NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set2), single strand read

treatment_protocol: GM12878 cells cultured in RPMI-1640 with 10% regular FBS were washed with PBS three times and then resuspended in methionine free RPMI-1640 (ThermoFisher Cat # A1451701) supplemented with 10% dialyzed FBS (ThermoFisher Cat #26400044). L-methionine was added to the cell culture to 100uM (control) or 1uM methionine (MR). 3×10^6 live cells were collected for intracellular metabolite profiling at 24 hours post MR. Thrity two NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunocompromised mice were subcutaneously xenotransplanted in the left flank with finely minced, 2-3mm^3 pieces of large cell lymphoma GM12878, and immediately placed on a control diet at time of implant. Tumor growth was monitored twice weekly, once tumor burden reached approximately 30-50mm^3, as measured by caliper, twenty four mice with similar tumor burden were randomized into three different collection timepoint groups; 7, 14 and 21 days (n=8 per timepoint). A tail vein pre-bleed was performed on all 24 mice after which 4 mice from each group were placed on a methionine restricted diet. Tumor burden and body weight were monitored twice weekly. Tail bleeds continued weekly unless animals were scheduled for collection for which a terminal cardiac bleed was performed. Also at time of sacrifice tumor was excised and collected three ways; flash frozen in LN2, placed in 10% neutral buffered formalin (moved to 70% EtOH after 24 hours), and placed in RNAlater. All animals were euthanized by CO2 asphyxiation at a flow rate 3.5 L/min. All blood was spun for serum and frozen at -20C and moved to -80C 24hours later.

value: lymphoblastoid cell

value: lymphocytes

value: WT

value: methionine restriction

tag: biomaterial provider


title: MM2 Tact DMSO (scATACseq)

description: Library name: MM2_act_DMSO


title: S14772Nr5_A549_siGOLM1-1_1

description:
Library name: siGOLM1-1_1
A549 cells transfected with siGOLM1-1, biological replicate 1


title: OVX8_SCI7 spinal cord biol rep 4

city: wenzhou

first: Quan

last: Zhou

state: zhejiang

address: Nanbaixiang street

department: Department of Spine Surgery

institute: The First Affiliated Hospital of Wenzhou Medical University

description:
Library name: OVX8_SCI7_4
Company group: treat; column name in processed matrices: OVX8_SCI7_4; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

data_processing:
Raw reads were quality-filtered according to the company report; the software list includes fastp v0.23.4 for sequencing data QC. Clean read statistics and mapping statistics are provided in the company report.
Clean reads were aligned to the Mus musculus GRCm39 reference genome. The company software list includes HISAT2 v2.2.1 for sequence alignment; exact alignment parameters were not available in the report folder reviewed.
Gene expression was quantified at the gene level using RSEM v1.3.3 according to the company differential-expression run parameter file (Exp_G_RSEM_TPM_20250407_185744).
Differential expression in the company report was performed with DESeq2 v1.42.0; downstream user analysis also compared DESeq2, edgeR, and limma-voom outputs.
Assembly: Mus musculus reference genome: GRCm39.
Supplementary files format and content: gene_count_matrix_annotation.tsv is a tab-delimited gene-level count matrix with annotations and sample/group columns.
Supplementary files format and content: gene_TPM_matrix_annotation.tsv and gene_FPKM_matrix_annotation.tsv are tab-delimited gene-level normalized expression matrices with annotations and sample/group columns.

source_name: spinal cord

growth_protocol: Female 8-week-old C57BL/6J wild-type mice were used. Spinal cord tissue was collected from the T9-T10 injury region, including approximately 0.5 cm rostral and caudal to the lesion site.

extract_protocol:
Total RNA was extracted from mouse spinal cord tissue and subjected to RNA quality assessment before library preparation. The exact RNA extraction kit/method and QC thresholds were not available in the report folder reviewed; confirm with the sequencing company if GEO requests this detail.
Paired-end RNA-seq libraries were prepared and sequenced on an Illumina platform. The exact library preparation kit was not available in the report folder reviewed. Read length was inferred as PE151 from raw reads and raw bases in the company QC table.
NOTE: Sequencing platform is filled as Illumina NovaSeq X Plus based on FASTQ header prefix LH; confirm with the sequencing company if exact instrument documentation is required.

treatment_protocol: SCI7: samples collected 7 days after T9-T10 clip-compression spinal cord injury. OVX2_SCI7: ovariectomy was performed, SCI was induced 2 weeks later, and tissue was collected 7 days after SCI. OVX8_SCI7: ovariectomy was performed, SCI was induced 8 weeks later, and tissue was collected 7 days after SCI.

value: spinal cord

value: Ovariectomy followed 8 weeks later by T9-T10 clip-compression SCI; tissue collected 7 days after SCI

tag: group code

tag: Sex

value: female

tag: age

value: 8 weeks

tag: strain

value: C57BL/6J wild type

tag: tissue region

value: T9-T10 spinal cord injury region, approximately 0.5 cm rostral and caudal to lesion site

tag: collection time_point

value: 7 days after SCI

tag: biological replicate


title: GM_MR_2

description: Library name: T_11

tag: cell line


title: MM1 Tact Mezi (scATACseq)

description: Library name: MM1_act_Mezi

tag: cell type

value: T-cell

value: Mezi


title: GM_MR_1

description: Library name: T_10

tag: treatment


title: S14772Nr4_A549_Control_4

description:
Library name: Control_4
A549 cells transfected with non-targeting control siRNA, biological replicate 4

value: Lung adenocarcinoma cells

value: Non-targeting control siRNA


title: OVX8_SCI7 spinal cord biol rep 3

description:
Library name: OVX8_SCI7_3
Company group: treat; column name in processed matrices: OVX8_SCI7_3; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

tag: tissue


title: MM1 Tact DMSO (scATACseq)

description: Library name: MM1_act_DMSO


title: OVX8_SCI7 spinal cord biol rep 2

description:
Library name: OVX8_SCI7_2
Company group: treat; column name in processed matrices: OVX8_SCI7_2; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.


title: S14772Nr3_A549_Control_3

description:
Library name: Control_3
A549 cells transfected with non-targeting control siRNA, biological replicate 3


title: Tex3,DMSO (ATAC)

description: Library name: Tex3_DMSO

extract_protocol:
Cells for ATACseq were prepared according to instructions from Novogene.
Five million cells were collected and cryopreserved prior to shipping to Novogene.


title: GM_CONTORL_3

description: Library name: T_09

value: control


title: S14772Nr2_A549_Control_2

description:
Library name: Control_2
A549 cells transfected with non-targeting control siRNA, biological replicate 2


title: GM_CONTORL_2

description: Library name: T_08


title: OVX8_SCI7 spinal cord biol rep 1

description:
Library name: OVX8_SCI7_1
Company group: treat; column name in processed matrices: OVX8_SCI7_1; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.


title: Tex3,Mezi (ATAC)

description: Library name: Tex3_480


title: GM_CONTORL_1

description: Library name: T_07


title: OVX2_SCI7 spinal cord biol rep 4

description:
Library name: OVX2_SCI7_4
Company group: control2; column name in processed matrices: OVX2_SCI7_4; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

value: Ovariectomy followed 2 weeks later by T9-T10 clip-compression SCI; tissue collected 7 days after SCI


title: S14772Nr1_A549_Control_1

description:
Library name: Control_1
A549 cells transfected with non-targeting control siRNA, biological replicate 1


title: Tex2,DMSO (ATAC)

description: Library name: Tex2_DMSO

value: DMSO


title: OVX2_SCI7 spinal cord biol rep 3

description:
Library name: OVX2_SCI7_3
Company group: control2; column name in processed matrices: OVX2_SCI7_3; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.


title: B2-7_3

city: Bogotá

first: Diego

middle: Alejandro

last: Suárez-García

department: Science department

country: Colombia

institute: IEIM

description: Library name: Sample6

data_processing:
Aligments conducted on Conda environment manager
Sequences were trimmed with trimmomatic (0.40-0)
Trimmed sequences were mapped to a human reference genome (GRCh38) using STAR software with these parameters:                                                                                --runThreadN 8 \  --outSAMtype BAM SortedByCoordinate \  --quantMode GeneCounts
Gene counts were normalized and analized for differential expression of genes using  edgeR (4.6.3) from the Bioconductor repository on R studio (2025.05.1 Build 513)
Assembly: GRCh38
Supplementary files format and content: A .tsv (Text Separated Values) file contains all raw counts of all samples. Gene IDs are on rows and samples on columns. File name: raw_count_matrix.tsv

growth_protocol: Cells were maintained in DMEM medium, 10% fetal bovine serum, and 1% penicillin/streptomycin. Cell cultures were incubated in a humidified environment at 37°C, CO₂ 5%.

extract_protocol:
Total RNA was extracted by triplicate for each condition by a standard TRIzol-Chloroform protocol
RNA libraries for RNA-Seq were prepared using Illumina TruSeq Stranded mRNA / Total RNA kit acording to manufacturer´s instructions

value: Glioblastoma

value: HEXA knockout


title: tumor_MR_3

description: Library name: T_06

source_name: lymphoblastoid cell xenograft

value: lymphoblastoid cell xenograft

value: lymphocytes

value: WT

value: dietary methionine restriction


title: Tex2,Mezi (ATAC)

description: Library name: Tex2_480


title: OVX2_SCI7 spinal cord biol rep 2

description:
Library name: OVX2_SCI7_2
Company group: control2; column name in processed matrices: OVX2_SCI7_2; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

value: spinal cord

value: female

value: 8 weeks


title: B2-7_2

description: Library name: Sample5


title: tumor_MR_2

description: Library name: T_05


title: Tex1,DMSO (ATAC)

description: Library name: Tex1_DMSO


title: OVX2_SCI7 spinal cord biol rep 1

description:
Library name: OVX2_SCI7_1
Company group: control2; column name in processed matrices: OVX2_SCI7_1; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

value: C57BL/6J wild type

value: T9-T10 spinal cord injury region, approximately 0.5 cm rostral and caudal to lesion site

value: 7 days after SCI


title: B2-7_1

description: Library name: Sample4


title: tumor_MR_1

description: Library name: T_04


title: SCI7 spinal cord biol rep 4

description:
Library name: SCI7_4
Company group: control1; column name in processed matrices: SCI7_4; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

value: T9-T10 clip-compression spinal cord injury; tissue collected 7 days after SCI


title: Tex1,Mezi (ATAC)

description: Library name: Tex1_480

value: T-cell

value: Mezi


title: U87MG WT_3

description: Library name: Sample3


title: Platelets, Healthy, Rep11

status: Public on Jul 05 2026

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2213 Garland Avenue South 9465

institute: Vanderbilt University

data_processing:
Raw sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7.
Trimmed reads were aligned to the hg38 reference genome and counted using STAR v2.7.9a with the `--quantMode GeneCounts` option.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Peripheral Blood Platelets

extract_protocol:
Samples were resuspended in 700 µl QIAzol Lysis Reagent (Qiagen GmbH, Hilden, Germany).
RNA was extracted from the platelet-QIAzol Lysis Reagent aliquots by application of the RNeasy Mini kit (Qiagen GmbH, Hilden, Germany; Cat: 1071023) according to the manufacturer’s recommendations.
Library preparation was completed using theNEBNext Ultra II Directional RNA Library Prep Kitand protocol (P/N: E7760L) per manufacturer recommendations.
RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by fragmentation using divalent cations under elevated temperature.
First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation were performed to generate the final cDNA library.

tag: disease state

value: healthy

value: Peripheral Blood Platelets


city: Basel

first: Atul

last: Sethi

address: Grenzacherstrasse 124

country: Switzerland

institute: Hoffmann-La Roche

description:
Library name: mouse_Ms4a3_12week_myeloid_CS_tomato_positive
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ and seq data was analyzed using cellranger mkfastq. Individual sample gene expression matrices were generated using the GRCm38 (mm10) mouse reference genome. Samples metadata were harmonized based on FAIR principles by transforming them into a common data model and mapping corresponding concepts to Roche Terminology System reference terminologies. Seq data were processed using Cellranger and mapped to the mouse genome (mm10).
The secondary analysis was performed with the scanpy package (version 1.9.6). Quality control measures included filtering out cells with high mitochondrial gene expression, cells with less than 200 or more than 10.000 expressed genes, and genes expressed in less than 3 cells.
The processed data were normalized per total cell counts and log1p-transformed. Highly variable genes (n=4000) were selected for downstream analyses.
Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (tSNE), and Uniform Manifold Approximation and Projection (UMAP) were employed for dimensionality reduction. Leiden clustering was performed to identify distinct cell populations within the dataset using default resolution 1. In order to overcome the batch effect between separate experiments, we used the scANVI method from the scArches package to integrate the two datasets. Downstream clustering and dimensionality reduction was performed on the latent space of the model.
Assembly: GRCm38 (mm10)
Supplementary files format and content: h5

source_name: Lung

growth_protocol: Throughout the studies, mice were kept under specific-pathogen-free conditions with continuous health monitoring.

extract_protocol:
Mice were euthanized by intraperitoneal injection of pentobarbital sodium (150 mg/kg; diluted 1:2 with 0.9% NaCl physiological) and analyzed ~16 h after the last CS exposure. After perfusion of the heart with PBS, for whole lung analysis, lungs were directly collected into 1 mL PBS (2% FBS). Lungs were processed using the mouse lung dissociation kit (#130-095-927, Miltenyi Biotec) according to the manufacturer's instructions (program 37C_m_LDK_1). After termination of the program, C tubes (#130-093-237, Miltenyi Biotec) were detached from the gentleMACS dissociator and centrifuged shortly at 1500 rpm. Pellets were resuspended in the same supernatant and filtered through a 70 μm cell strainer (#CLS431751, Sigma-Aldrich) into a 50 mL tube. After centrifugation at 1500 rpm for 2 min, the supernatant was discarded and the pellets were resuspended with 1 mL ACK lysis buffer (#A1049201, Thermo Fisher Scientific) for 3-5 min. Again, the suspension was filtered through a 70 μm cell strainer (#CLS431751, Sigma-Aldrich) and spun at 1500 rpm for 2 min. The supernatant was discarded and cells were resuspended in 0.5-1 mL PBS (2% FBS) and used for subsequent flow cytometry experiments. Per experiment, 100.000 (12+8 weeks experiment) or 250.000 cells (4 and 12 weeks experiments) were FACS-sorted (Myeloid cells: viable CD45+ single cells; excluded CD11c/CD11b double-negative cells = considered as non-myeloid cells; AM: live CD45+CD11c+SiglecF+ cells).
According to the manufacturer's instructions (Chromium Next GEM Single Cell 3' Kit v3.1 16 rxns PN-1000-268; Chromium Next GEM Chip G Single Cell Kit, 48 rxns PN- 1000120, 10x Genomics), 12.000 cells per sample (with a viability of more than 80%) were loaded onto the 10X genomics device (Chromium controller, 10x Genomics). The generated cDNA samples were submitted to Roche internal seq facilities for seq using the 10x Genomics' scRNA seq technology. ScRNA seq was performed using the Chromium Next GEM Single Cell 3' reagent kit v3.1 from 10X genomics according to the user guide Ref CG000315 Rev F. Targeted cell recovery of 8000 cells. Samples were indexed using Dual Index Kit TT Set A. Single Cell 3' gene expression libraries were sequenced using standard Illumina paired-end constructs beginning P5 and P7. Seq these libraries produces a standard Illumina BCL data output folder. Seq was performed using the NovaSeq6000 instrument from Illumina. Seq depth minimum of 20000 read pairs per cell, paired end dual indexing with a seq read cycles of 28-10-10-90. Libraries were quantified, normalized and pooled followed by denaturation and dilution according to the Illumina recommendations for the NovaSeq 6000 of 300 pM together with a 1% PhiX concentration.

treatment_protocol: In vivo room air or cigarette smoke exposure

value: Lung

value: Myeloid cell

value: Cigarette Smoke


description:
Library name: mouse_Ms4a3_12week_myeloid_RA_tomato_negative
10x Genomics

value: Room Air


title: Platelets, Healthy, Rep7


title: Tumor control_3

description: Library name: T_03

value: lymphoblastoid cell xenograft

value: lymphocytes

value: WT

value: control


title: SCI7 spinal cord biol rep 3

description:
Library name: SCI7_3
Company group: control1; column name in processed matrices: SCI7_3; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

value: spinal cord

value: female

value: 8 weeks


title: U87MG WT_2

description: Library name: Sample2

value: Glioblastoma


title: Tact3,DMSO (ATAC)

description: Library name: Tact3_DMSO

value: DMSO


title: Tact2,DMSO (ATAC)

description: Library name: Tact2_DMSO

value: T-cell


title: Tumor control_2

description: Library name: T_02


title: SCI7 spinal cord biol rep 2

description:
Library name: SCI7_2
Company group: control1; column name in processed matrices: SCI7_2; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.

value: T9-T10 clip-compression spinal cord injury; tissue collected 7 days after SCI

value: C57BL/6J wild type

value: T9-T10 spinal cord injury region, approximately 0.5 cm rostral and caudal to lesion site

value: 7 days after SCI


title: U87MG WT_1

description: Library name: Sample1


title: Tact1,DMSO (ATAC)

description: Library name: Tact1_DMSO


title: Tumor control_1

description: Library name: T_01


title: Bone marrow aspirate from B-ALL patient 3 at diagnosis

status: Public on Jul 03 2026

city: Jinan

first: Yunpeng

last: Dai

address: Department of Pediatric Hematology and Endocrinology 324 Jingwu Weiqi Road

institute: Shandong Provincial Hospital affiliated to Shandong First Medical University

description: Library name: ALL3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the BD Rhapsody™ Sequence Analysis Pipeline v1.9.1(https://www.bdbiosciences.com/en-us/products/software/rhapsody-sequence-analysis-pipeline)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Single cells capture were perfomed according to the manufacturers protocol (supported by Beijing CHUPO Medical Laboratory Co. Ltd). Briefly, about 20,000 cells and capture magnetic beads were loaded onto BD Rhapsody cartridges in turn. Following washed, cells were lysed, and the capture beads combined with polyA mRNA were retrieved and washed.
cDNA synthesis and library preparation were perfomed according to the manufacturers protocol (supported by Beijing CHUPO Medical Laboratory Co. Ltd). Briefly,  after reverse transcription and ExoI digestion, whole-transcriptome library preparation was performed using the BD Rhapsody™ whole transcriptome analysis (WTA) amplification kit (BD Biosciences, USA). Sequencing libraries were analyzed with Equalbit 1 × dsDNA HS Assay Kit (Vazyme, China) and Standard (S2) Cartridge Kit (Bioptic, Taiwan, China) for quality control.

value: Bone marrow


title: Bone marrow aspirate from B-ALL patient 4 at relapse

department: Department of Pediatric Hematology and Endocrinology

description: Library name: ALL4


title: mm468_scCUT&Tag_10x_h3k27me3

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: Library name: mm468_scCUT_Tag_10x_h3k27me3

data_processing:
Raw fastq files were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Assembly: hg38
Supplementary files format and content: fragment files of DNA counts :  N59N64_MM468BC_K27me3.fragments.tsv.gz
Supplementary files format and content: fragment file indexes: N59N64_MM468BC_K27me3.fragments.tsv.gz.tbi
Supplementary files format and content: Pseudobulk bigwig (CPM-normalized): N59N64_MM468BC_K27me3.bigwig
Library strategy: CUT&Tag

growth_protocol: MDA-MB-468 cells (American Type Culture Collection (ATCC), HTB-132) were maintained in DMEM (Gibco-BRL, 11966025) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, 10500064) and cultured in a humidified 5% CO2 atmosphere at 37 °C.

extract_protocol:
Nuclei from 500000 MDA-MB-468 cells are extracted on ice using nuclear extraction buffer (20mM HEPES pH7.5, 50mM KCl, 20% Glycerol, 0.5mM Spermidine, 1X Protease Inhibitor Cocktail, 2% BSA, 0.1% NP-40, 0.01% Digitonin).
10x scCUT&Tag protocol as described in (Moutaux & Schwager et al., 2025)

value: epithelial

value: no

tag: library type

value: DNA


title: Bone marrow aspirate from B-ALL patient 2 at diagnosis

description: Library name: ALL2


title: SCI7 spinal cord biol rep 1

description:
Library name: SCI7_1
Company group: control1; column name in processed matrices: SCI7_1; tissue region: T9-T10 spinal cord lesion area with approximately 0.5 cm rostral and caudal margins.


title: H3K27ac_ChIPseq, GBMT-V001

first: Mahinur

last: Mattohti

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Assembly: hg19
Supplementary files format and content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14

extract_protocol:
Crosslinked samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

value: GBM tumor

tag: chip antibody


title: H3K27ac_ChIPseq, GBMT-U087


title: H3K27ac_ChIPseq, GBMT-2522


title: H3K27ac_ChIPseq, GBMT-M001


title: H3K27ac_ChIPseq, GBMT-2521


title: H3K27ac_ChIPseq, GBMT-1835


title: H3K27ac_ChIPseq, GBMT-1837


title: H3K27ac_ChIPseq, GBMT-1834


title: H3K27ac_ChIPseq, GBMT-1833


title: H3K27ac_ChIPseq, GBMT-0531


title: Mouse, HLI+GNPs-pIL--4 treated, 14 Days,

city: Beijing

first: peng

last: zhang

state: Beijing

address: Peking University Medical Industrial Park

institute: Peking University

description: Library name: HLI+GNPs-pIL-4

data_processing:
Raw paired-end sequencing reads were processed using the 10x Genomics Cell Ranger pipeline (version 7.1.0). Demultiplexing, alignment to the mouse reference genome (mm10/GRCm39), barcode counting, and UMI quantification were performed using cellranger count. The output filtered feature-barcode matrix containing gene expression counts for cell-associated barcodes is provided as the processed data.
Assembly: mm10 (GRCm39)
Supplementary files format and content: Filtered feature-barcode matrix in 10x Genomics format. Contains three gzipped files: 1) barcodes.tsv.gz(cell barcodes), 2) features.tsv.gz(gene identifiers), and 3) matrix.mtx.gz(UMI count matrix). This matrix represents the combined cells from the GNPs-pIL-4 treated sample.
Supplementary files format and content: Tab-separated values files and matrix files from 10x Genomics Cell Ranger output

source_name: Gastrocnemius muscle

growth_protocol: C57BL/6J mice were maintained under specific pathogen-free conditions with free access to food and water.

extract_protocol:
Fourteen days after HLI surgery and GNPs-pIL-4 treatment, mice were euthanized, and gastrocnemius muscle tissues were harvested. A total of 0.6 g of muscle tissue was collected and immediately immersed in ice-cold tissue preservation solution. Samples were transferred on ice to the processing station, where single-cell suspensions were prepared using a tissue dissociation system (gentleMACS Octo, Miltenyi Biotec GmbH) in accordance with the protocol of the muscle tissue dissociation kit (130-098-305, Miltenyi Biotec, Germany).
Single-cell transcriptome libraries were constructed using the 10x Genomics 3' single-cell RNA-seq platform following the manufacturer's instructions.

treatment_protocol: Mice were subjected to femoral artery ligation to establish hindlimb ischemia (HLI) and then received intramuscular injections of GNPs-pIL-4.

value: Gastrocnemius muscle

value: Mixed cells

value: Hindlimb ischemia with GNPs-pIL-4 intramuscular injection


title: H3K27ac_ChIPseq, GBMT-1830


title: H3K27ac_ChIPseq, GBMT-1832


title: H3K27ac_ChIPseq, GBMT-0520


title: H3K27ac_ChIPseq, GBMT-1831


title: H3K27ac_ChIPseq, GBMT-0518


title: H3K27ac_ChIPseq, GBMT-0517


title: H3K27ac_ChIPseq, GBMT-0511


title: H3K27ac_ChIPseq, GBMT-0392


title: H3K27ac_ChIPseq, GBMT-0359


title: PA1577-1

status: Public on Jul 06 2026

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1577.xlsx

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas aeruginosa (NC_002516.2)
Supplementary files format and content: xlsx files were generated from RNA-seq, containing the differential expressional genes.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: RNA-seq(LB)

extract_protocol:
The Pseudomonas aeruginosa PAO1 wild type strain and the HP mutants were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

treatment_protocol: grow until mid-log phase

value: Pseudomonas aeruginosa PAO1

tag: genotype

value: PA1577 mutant

value: grow until mid-log phase in LB


title: H3K27ac_ChIPseq, GBMT-0358


title: H3K27ac_ChIPseq, GBMT-0352


title: H3K27ac_ChIPseq, GBMT-0246


title: SCRC-T265_Input DNA

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14 and MACS2

growth_protocol: All cell lines were expanded and maintained in specified growth medium from ATCC or MDACC.

value: MPNST cancer cell line


title: SCRC-T265_H3K79me2_ChIPseq


title: SCRC-T265_H3K9me3_ChIPseq


title: SCRC-T265_H3K4me1_ChIPseq


title: SCRC-T265_H3K27ac_ChIPseq


title: SCRC-ST88_Input DNA


title: SCRC-ST88_H3K4me3_ChIPseq


title: SCRC-ST88_H3K79me2_ChIPseq


title: SCRC-ST88_H3K27ac_ChIPseq


title: SCRC-ST26_Input DNA


title: SCRC-ST26_H3K27me3_ChIPseq


title: SCRC-ST88_H3K4me1_ChIPseq


title: SCRC-ST26_H3K4me3_ChIPseq


title: SCRC-ST26_H3K79me2_ChIPseq


title: SCRC-ST26_H3K4me1_ChIPseq


title: SCRC-S462_Input DNA


title: SCRC-ST26_H3K9me3_ChIPseq


title: SCRC-S462_H3K27me3_ChIPseq


title: SCRC-S462_H3K4me3_ChIPseq


title: SCRC-S462_H3K27ac_ChIPseq


title: SCRC-S462_H3K9me3_ChIPseq


title: SCRC-M724_Input DNA


title: SCRC-M724_H3K27me3_ChIPseq


title: SCRC-M724_H3K79me2_ChIPseq


title: SCRC-M724_H3K4me3_ChIPseq


title: SCRC-M642_Input DNA


title: SCRC-M724_H3K27ac_ChIPseq


title: SCRC-M642_H3K27me3_ChIPseq


title: SCRC-M642_H3K4me3_ChIPseq


title: SCRC-M642_H3K79me2_ChIPseq


title: SCRC-M724_H3K9me3_ChIPseq


title: SCRC-M642_H3K27ac_ChIPseq


title: SCRC-M642_H3K9me3_ChIPseq


title: SCRC-M642_H3K4me1_ChIPseq


title: Bone marrow aspirate from B-ALL patient 1 at diagnosis

description: Library name: ALL1


title: SCRC-M381_Input DNA


title: SCRC-M381_H3K27me3_ChIPseq


title: SCRC-M381_H3K4me3_ChIPseq


title: SCRC-M381_H3K9me3_ChIPseq


title: SCRC-M381_H3K27ac_ChIPseq


title: PAAD-P053_Input DNA

value: Pancreatic cancer cell line


title: SCRC-M381_H3K4me1_ChIPseq


title: PAAD-P053_H3K27me3_ChIPseq


title: PAAD-P053_H3K4me3_ChIPseq


title: PAAD-P053_H3K79me2_ChIPseq


title: PAAD-P053_H3K27ac_ChIPseq


title: PAAD-P053_H3K4me1_ChIPseq


title: PAAD-P034_H3K27me3_ChIPseq


title: PAAD-P053_H3K9me3_ChIPseq


title: PAAD-P034_Input DNA


title: PAAD-P034_H3K27ac_ChIPseq


title: PAAD-P034_H3K4me1_ChIPseq


title: PAAD-P034_H3K9me3_ChIPseq


title: PAAD-P034_H3K79me2_ChIPseq


title: PAAD-P033_Input DNA


title: PAAD-P033_H3K27me3_ChIPseq


title: PAAD-P033_H3K4me3_ChIPseq


title: PAAD-P033_H3K79me2_ChIPseq


title: PAAD-P033_H3K27ac_ChIPseq


title: PAAD-P033_H3K9me3_ChIPseq


title: SCRC-T265_H3K4me3_ChIPseq


title: PAAD-P021_H3K27me3_ChIPseq


title: PAAD-P033_H3K4me1_ChIPseq


title: PAAD-P021_Input DNA


title: SCRC-ST88_H3K9me3_ChIPseq


title: PAAD-P021_H3K4me3_ChIPseq


title: PAAD-P021_H3K79me2_ChIPseq


title: PAAD-P021_H3K27ac_ChIPseq


title: SCRC-ST26_H3K27ac_ChIPseq


title: PAAD-P021_H3K9me3_ChIPseq


title: PAAD-P021_H3K4me1_ChIPseq


title: PAAD-P016_Input DNA


title: SCRC-S462_H3K79me2_ChIPseq


title: PAAD-P016_H3K27me3_ChIPseq


title: PAAD-P016_H3K4me3_ChIPseq


title: PAAD-P016_H3K27ac_ChIPseq


title: PAAD-P016_H3K9me3_ChIPseq


title: PAAD-P016_H3K4me1_ChIPseq


title: PAAD-P016_H3K79me2_ChIPseq


title: PAAD-P013_H3K27me3_ChIPseq


title: PAAD-P013_H3K4me3_ChIPseq


title: PAAD-P013_H3K79me2_ChIPseq


title: PAAD-P013_H3K27ac_ChIPseq


title: PAAD-P011_Input DNA


title: PAAD-P013_H3K4me1_ChIPseq


title: PAAD-P011_H3K27me3_ChIPseq


title: PAAD-P011_H3K4me3_ChIPseq


title: PAAD-P011_H3K27ac_ChIPseq


title: PAAD-P011_H3K9me3_ChIPseq


title: PAAD-P011_H3K4me1_ChIPseq


title: PAAD-P010_H3K27me3_ChIPseq


title: PAAD-P010_H3K79me2_ChIPseq


title: PAAD-P010_H3K4me3_ChIPseq


title: PAAD-P010_H3K27ac_ChIPseq


title: PAAD-P008_Input DNA


title: PAAD-P010_H3K4me1_ChIPseq


title: PAAD-P008_H3K27me3_ChIPseq


title: PAAD-P010_H3K9me3_ChIPseq


title: PAAD-P008_H3K79me2_ChIPseq


title: PAAD-P008_H3K4me3_ChIPseq


title: PAAD-P008_H3K9me3_ChIPseq


title: PAAD-P008_H3K4me1_ChIPseq


title: PAAD-P002_Input DNA


title: PAAD-P002_H3K27me3_ChIPseq


title: PAAD-P002_H3K4me3_ChIPseq


title: PAAD-P002_H3K79me2_ChIPseq


title: PAAD-P002_H3K27ac_ChIPseq


title: PAAD-P002_H3K4me1_ChIPseq


title: PAAD-P001_Input DNA


title: PAAD-P001_H3K27me3_ChIPseq


title: PAAD-P001_H3K4me3_ChIPseq


title: PAAD-P001_H3K27ac_ChIPseq


title: PAAD-P001_H3K79me2_ChIPseq


title: PAAD-P001_H3K9me3_ChIPseq


title: OVCA-V037_H3K27me3_ChIPseq

value: Ovarian cancer cell line


title: OVCA-V037_H3K4me3_ChIPseq


title: OVCA-V037_H3K79me2_ChIPseq


title: OVCA-V037_H3K27ac_ChIPseq


title: OVCA-V037_H3K9me3_ChIPseq


title: OVCA-V037_H3K4me1_ChIPseq


title: OVCA-V027_Input DNA


title: Microbiota of stool from K12EM  control

city: Antalya

first: Ceren

last: Hangul

address: Dumlupınar street

country: Turkey

institute: Akdeniz University

description:
18s rRNA V2-V9 sequencing of human stool
K12EM

data_processing:
Demultiplexing: From raw to demultiplexed fastq files please contact Ceren Hangul (cerenhangul@hotmail.com)
Quality check: qiime demux summarize --i-data trim-seqs.qza --o-visualization quality --p-n 100000
Quality trimming of first raws sequences and ASV table creation: qiime dada2 denoise-single --i-demultiplexed-seqs  single_end_demux.qza --p-trunc-len 250 --o-table Featuredada.qza --o-representative-sequences data-trunc.qza --o-denoising-stats denoising-stats.qza --p-n-threads 1 --verbose
Quality trimming of second raws sequences and ASV table creation: qiime dada2 denoise-single --i-demultiplexed-seqs  single-end-demux-repeat.qza --p-trunc-len 250 --o-table Featuredada1.qza --o-representative-sequences data-trunc1.qza --o-denoising-stats denoising-stats1.qza --p-n-threads 1 --verbose
Merge of sequences in output of previous quality trimming: qiime feature-table merge-seqs --i-data data-trunc.qza --i-data data-trunc1.qza --o-merged-data rep-seqs.qza
Discard sequences from host (Homo Sapiens): bowtie2 -x GRCh38_noalt_as/GRCh38_noalt_as -U dna-sequences.fasta --un filtered.fasta -S seq_human_SAM.txt  -f -p 5
Taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads import_filtered.qza --o-classification taxonomy.qza --p-n-jobs 8 --p-reads-per-batch 1000 --verbose
Further analyses: R phyloseq package
Assembly: SILVA 138-99 nb classifier
Supplementary files format and content: feature-table1.csv: CSV text file containing the abundance table of first raw sequences
Supplementary files format and content: feature-table2.csv: CSV text file containing the abundance table of second raw sequences
Supplementary files format and content: taxonomy.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: filtered.fasta: fasta file containing the reference sequences used for taxonomy classification

source_name: Stool

growth_protocol: Samples were sored at -80 °C before the DNA extraction. After extraction, DNA were frozen at -20 °C until sequencing.

extract_protocol:
Genomic DNA from stool was extracted using the QIAamp Fast DNA Stool Mini Kit (Qiagen, Hilden, Germany)
Amplicon libraries of the V2-V9 16S rRNA hypervariable regions were prepared. The size and concentration of the final sequencing library, formed by pooling the barcoded amplicons in equimolar concentrations, were determined using the Bioanalyzer High Sensitivity Chip (Agilent Technologies, Santa Clara, CA, USA).
Amplicons of the variable V2-V9 region of the bacterial 16S rRNA gene were sequenced in single

value: Stool

value: Subject not affected by FSHD


title: OVCA-V027_H3K4me1_ChIPseq


title: OVCA-V026_Input DNA


title: OVCA-V026_H3K27me3_ChIPseq


title: OVCA-V026_H3K79me2_ChIPseq


title: OVCA-V026_H3K9me3_ChIPseq


title: OVCA-V023_Input DNA


title: OVCA-V023_H3K27me3_ChIPseq


title: OVCA-V023_H3K4me3_ChIPseq


title: OVCA-V023_H3K79me2_ChIPseq


title: OVCA-V023_H3K27ac_ChIPseq


title: OVCA-V023_H3K9me3_ChIPseq


title: OVCA-V023_H3K4me1_ChIPseq


title: PAAD-P013_Input DNA


title: PAAD-P013_H3K9me3_ChIPseq


title: OVCA-V020_Input DNA


title: PAAD-P011_H3K79me2_ChIPseq


title: OVCA-V020_H3K27me3_ChIPseq


title: PAAD-P010_Input DNA


title: OVCA-V020_H3K4me3_ChIPseq


title: OVCA-V020_H3K79me2_ChIPseq


title: OVCA-V020_H3K27ac_ChIPseq


title: OVCA-V020_H3K9me3_ChIPseq


title: PAAD-P008_H3K27ac_ChIPseq


title: OVCA-V020_H3K4me1_ChIPseq


title: OVCA-V017_Input DNA


title: OVCA-V017_H3K27me3_ChIPseq


title: OVCA-V017_H3K27ac_ChIPseq


title: PAAD-P002_H3K9me3_ChIPseq


title: OVCA-V014_H3K27me3_ChIPseq


title: OVCA-V017_H3K4me1_ChIPseq


title: OVCA-V017_H3K4me3_ChIPseq


title: OVCA-V014_H3K4me3_ChIPseq


title: OVCA-V014_H3K79me2_ChIPseq


title: OVCA-V037_Input DNA


title: OVCA-V014_H3K27ac_ChIPseq


title: PAAD-P001_H3K4me1_ChIPseq


title: OVCA-V013_Input DNA


title: OVCA-V014_H3K4me1_ChIPseq


title: OVCA-V014_H3K9me3_ChIPseq


title: OVCA-V013_H3K27me3_ChIPseq


title: OVCA-V013_H3K4me3_ChIPseq


title: OVCA-V013_H3K79me2_ChIPseq


title: OVCA-V013_H3K9me3_ChIPseq


title: OVCA-V013_H3K27ac_ChIPseq


title: OVCA-V010_H3K27me3_ChIPseq


title: OVCA-V013_H3K4me1_ChIPseq


title: OVCA-V010_Input DNA


title: OVCA-V010_H3K4me3_ChIPseq


title: OVCA-V010_H3K79me2_ChIPseq


title: OVCA-V027_H3K4me3_ChIPseq


title: OVCA-V027_H3K27me3_ChIPseq


title: OVCA-V010_H3K27ac_ChIPseq


title: OVCA-V010_H3K9me3_ChIPseq


title: OVCA-V027_H3K27ac_ChIPseq


title: OVCA-V010_H3K4me1_ChIPseq


title: OVCA-V009_Input DNA


title: OVCA-V009_H3K27me3_ChIPseq


title: OVCA-V009_H3K4me3_ChIPseq


title: OVCA-V009_H3K27ac_ChIPseq


title: OVCA-V009_H3K79me2_ChIPseq


title: OVCA-V009_H3K9me3_ChIPseq


title: OVCA-V008_H3K27me3_ChIPseq


title: OVCA-V008_Input DNA


title: OVCA-V009_H3K4me1_ChIPseq


title: OVCA-V008_H3K79me2_ChIPseq


title: OVCA-V008_H3K4me3_ChIPseq


title: OVCA-V008_H3K27ac_ChIPseq


title: OVCA-V026_H3K27ac_ChIPseq


title: OVCA-V008_H3K9me3_ChIPseq


title: OVCA-V008_H3K4me1_ChIPseq


title: OVCA-V007_H3K27me3_ChIPseq


title: OVCA-V007_Input DNA


title: OVCA-V007_H3K4me3_ChIPseq


title: OVCA-V007_H3K79me2_ChIPseq


title: OVCA-V007_H3K27ac_ChIPseq


title: OVCA-V007_H3K9me3_ChIPseq


title: OVCA-V026_H3K4me1_ChIPseq


title: OVCA-V007_H3K4me1_ChIPseq


title: M-WM88_Input DNA

value: Melanoma cancer cell line


title: M-WM88_H3K4me3_ChIPseq


title: M-WM88_H3K27me3_ChIPseq


title: M-WM88_H3K79me2_ChIPseq


title: M-WM88_H3K27ac_ChIPseq


title: M-WM793B_H3K27me3_ChIPseq


title: M-WM793B_Input DNA


title: M-WM88_H3K4me1_ChIPseq


title: M-WM88_H3K9me3_ChIPseq


title: M-WM793B_H3K4me3_ChIPseq


title: M-WM793B_H3K27ac_ChIPseq


title: M-WM793B_H3K79me2_ChIPseq


title: M-WM793B_H3K9me3_ChIPseq


title: M-WM239B_Input DNA


title: M-WM793B_H3K4me1_ChIPseq


title: M-WM239B_H3K27me3_ChIPseq


title: M-WM239B_H3K79me2_ChIPseq


title: M-WM239B_H3K4me3_ChIPseq


title: M-WM239B_H3K27ac_ChIPseq


title: M-UACC62_Input DNA


title: M-UACC62_H3K27me3_ChIPseq


title: M-UACC62_H3K4me3_ChIPseq


title: M-UACC62_H3K27ac_ChIPseq


title: M-UACC62_H3K79me2_ChIPseq


title: M-UACC62_H3K9me3_ChIPseq


title: M-UACC62_H3K4me1_ChIPseq


title: M-SKMEL5_Input DNA


title: M-SKMEL5_H3K27me3_ChIPseq


title: M-SKMEL5_H3K4me3_ChIPseq


title: M-SKMEL5_H3K79me2_ChIPseq


title: M-SKMEL5_H3K27ac_ChIPseq


title: M-SKMEL5_H3K9me3_ChIPseq


title: M-SKMEL5_H3K4me1_ChIPseq


title: M-MEWO_Input DNA

source_name: M-MEWO

value: M-MEWO


title: M-MEWO_H3K27me3_ChIPseq


title: M-MEWO_H3K4me3_ChIPseq


title: M-MEWO_H3K27ac_ChIPseq


title: M-MEWO_H3K79me2_ChIPseq


title: M-MEWO_H3K9me3_ChIPseq


title: M-940_Input DNA


title: M-940_H3K27me3_ChIPseq


title: M-940_H3K4me3_ChIPseq


title: M-940_H3K79me2_ChIPseq


title: M-940_H3K27ac_ChIPseq


title: M-940_H3K4me1_ChIPseq


title: M-940_H3K9me3_ChIPseq


title: M-Hs934_Input DNA


title: M-Hs934_H3K27me3_ChIPseq


title: M-Hs934_H3K4me3_ChIPseq


title: M-Hs934_H3K79me2_ChIPseq


title: M-Hs934_H3K9me3_ChIPseq


title: M-Hs934_H3K4me1_ChIPseq


title: M-G361_H3K27me3_ChIPseq


title: M-G361_Input DNA


title: M-G361_H3K4me3_ChIPseq


title: M-G361_H3K79me2_ChIPseq


title: M-G361_H3K27ac_ChIPseq


title: M-G361_H3K9me3_ChIPseq


title: M-G361_H3K4me1_ChIPseq


title: M-Hs934_H3K27ac_ChIPseq


title: M-MEWO_H3K4me1_ChIPseq


title: M-CHL1_Input DNA


title: M-CHL1_H3K27me3_ChIPseq


title: M-CHL1_H3K4me3_ChIPseq


title: M-CHL1_H3K79me2_ChIPseq


title: M-CHL1_H3K4me1_ChIPseq


title: M-CHL1_H3K9me3_ChIPseq


title: M-A375_Input DNA


title: M-A375_H3K79me2_ChIPseq


title: M-A375_H3K27me3_ChIPseq


title: M-A375_H3K4me3_ChIPseq


title: M-A375_H3K27ac_ChIPseq


title: M-A375_H3K9me3_ChIPseq


title: M-A2058_Input DNA


title: M-A2058_H3K27me3_ChIPseq


title: M-A2058_H3K79me2_ChIPseq


title: M-A2058_H3K4me3_ChIPseq


title: M-A375_H3K4me1_ChIPseq


title: M-A2058_H3K27ac_ChIPseq


title: M-A2058_H3K9me3_ChIPseq


title: M-A2058_H3K4me1_ChIPseq


title: M-96_Input DNA


title: M-96_H3K79me2_ChIPseq


title: M-96_H3K27ac_ChIPseq


title: M-84_Input DNA


title: M-84_H3K27me3_ChIPseq


title: M-84_H3K4me3_ChIPseq


title: M-84_H3K79me2_ChIPseq


title: M-96_H3K4me3_ChIPseq


title: SCRC-S462_H3K4me1_ChIPseq


title: M-96_H3K4me1_ChIPseq


title: M-84_H3K27ac_ChIPseq


title: M-84_H3K9me3_ChIPseq


title: M-96_H3K27me3_ChIPseq


title: M-84_H3K4me1_ChIPseq


title: M-61_Input DNA


title: M-61_H3K27me3_ChIPseq


title: M-61_H3K4me3_ChIPseq


title: M-61_H3K27ac_ChIPseq


title: M-61_H3K9me3_ChIPseq


title: M-57_Input DNA


title: M-57_H3K27me3_ChIPseq


title: M-61_H3K79me2_ChIPseq


title: M-61_H3K4me1_ChIPseq


title: M-57_H3K4me3_ChIPseq


title: M-57_H3K79me2_ChIPseq


title: M-57_H3K27ac_ChIPseq


title: M-57_H3K4me1_ChIPseq


title: M-57_H3K9me3_ChIPseq


title: M-52_Input DNA


title: M-52_H3K27me3_ChIPseq


title: M-52_H3K4me3_ChIPseq


title: M-52_H3K79me2_ChIPseq


title: M-52_H3K4me1_ChIPseq


title: M-52_H3K9me3_ChIPseq


title: M-52_H3K27ac_ChIPseq


title: M-48_Input DNA


title: M-48_H3K4me3_ChIPseq


title: M-48_H3K79me2_ChIPseq


title: M-48_H3K27ac_ChIPseq


title: M-48_H3K4me1_ChIPseq


title: M-22_Input DNA


title: M-22_H3K27me3_ChIPseq


title: M-22_H3K79me2_ChIPseq


title: M-22_H3K27ac_ChIPseq


title: M-22_H3K4me3_ChIPseq


title: M-22_H3K9me3_ChIPseq


title: M-22_H3K4me1_ChIPseq


title: M-12_Input DNA


title: M-12_H3K4me3_ChIPseq


title: M-12_H3K27me3_ChIPseq


title: M-12_H3K79me2_ChIPseq


title: M-CHL1_H3K27ac_ChIPseq


title: M-12_H3K27ac_ChIPseq


title: M-12_H3K9me3_ChIPseq


title: M-12_H3K4me1_ChIPseq


title: LUNG-L069_Input DNA

value: Lung cancer cell line


title: LUNG-L069_H3K4me3_ChIPseq


title: LUNG-L069_H3K27me3_ChIPseq


title: LUNG-L069_H3K27ac_ChIPseq


title: LUNG-L069_H3K9me3_ChIPseq


title: LUNG-L062_Input DNA


title: LUNG-L062_H3K27me3_ChIPseq


title: LUNG-L062_H3K4me3_ChIPseq


title: LUNG-L062_H3K79me2_ChIPseq


title: LUNG-L062_H3K27ac_ChIPseq


title: LUNG-L046_Input DNA


title: LUNG-L062_H3K9me3_ChIPseq


title: LUNG-L062_H3K4me1_ChIPseq


title: LUNG-L046_H3K27me3_ChIPseq


title: LUNG-L046_H3K4me3_ChIPseq


title: LUNG-L046_H3K79me2_ChIPseq


title: LUNG-L046_H3K4me1_ChIPseq


title: LUNG-L046_H3K9me3_ChIPseq


title: LUNG-L044_Input DNA


title: LUNG-L044_H3K4me3_ChIPseq


title: LUNG-L046_H3K27ac_ChIPseq


title: LUNG-L044_H3K27me3_ChIPseq


title: LUNG-L044_H3K27ac_ChIPseq


title: LUNG-L044_H3K9me3_ChIPseq


title: LUNG-L036_H3K27me3_ChIPseq


title: LUNG-L036_H3K4me3_ChIPseq


title: LUNG-L036_Input DNA


title: LUNG-L044_H3K79me2_ChIPseq


title: LUNG-L036_H3K79me2_ChIPseq


title: LUNG-L036_H3K27ac_ChIPseq


title: LUNG-L036_H3K9me3_ChIPseq


title: LUNG-L029_Input DNA


title: LUNG-L029_H3K27me3_ChIPseq


title: LUNG-L029_H3K27ac_ChIPseq


title: LUNG-L029_H3K9me3_ChIPseq


title: LUNG-L029_H3K4me3_ChIPseq


title: LUNG-L027_Input DNA


title: LUNG-L027_H3K27me3_ChIPseq


title: LUNG-L029_H3K4me1_ChIPseq


title: LUNG-L029_H3K79me2_ChIPseq


title: LUNG-L027_H3K27ac_ChIPseq


title: LUNG-L020_H3K27me3_ChIPseq


title: LUNG-L027_H3K9me3_ChIPseq


title: LUNG-L020_Input DNA


title: LUNG-L020_H3K4me3_ChIPseq


title: LUNG-L020_H3K79me2_ChIPseq


title: LUNG-L020_H3K27ac_ChIPseq


title: LUNG-L027_H3K4me3_ChIPseq


title: LUNG-L011_Input DNA


title: LUNG-L011_H3K27me3_ChIPseq


title: LUNG-L011_H3K4me3_ChIPseq


title: LUNG-L011_H3K27ac_ChIPseq


title: LUNG-L011_H3K79me2_ChIPseq


title: LUNG-L011_H3K9me3_ChIPseq


title: LUNG-L011_H3K4me1_ChIPseq


title: LUNG-L009_Input DNA


title: LUNG-L009_H3K27me3_ChIPseq


title: LUNG-L009_H3K4me3_ChIPseq


title: LUNG-L009_H3K79me2_ChIPseq


title: LUNG-L009_H3K27ac_ChIPseq


title: LUNG-L009_H3K9me3_ChIPseq


title: LUNG-L009_H3K4me1_ChIPseq


title: HNSC-U6XX_Input DNA

value: Head & Neck cancer cell line


title: HNSC-U6XX_H3K27me3_ChIPseq


title: HNSC-U6XX_H3K4me3_ChIPseq


title: HNSC-U6XX_H3K4me1_ChIPseq


title: HNSC-U6XX_H3K79me2_ChIPseq


title: HNSC-U6XX_H3K27ac_ChIPseq


title: HNSC-U4XX_H3K4me3_ChIPseq


title: HNSC-U4XX_Input DNA


title: HNSC-U47X_Input DNA


title: HNSC-U47X_H3K4me3_ChIPseq


title: HNSC-U47X_H3K79me2_ChIPseq


title: HNSC-U25X_Input DNA


title: HNSC-U25X_H3K27me3_ChIPseq


title: HNSC-U25X_H3K4me3_ChIPseq


title: HNSC-U25X_H3K79me2_ChIPseq


title: HNSC-U25X_H3K27ac_ChIPseq


title: HNSC-U22B_Input DNA


title: HNSC-U25X_H3K4me1_ChIPseq


title: HNSC-U22B_H3K4me3_ChIPseq


title: HNSC-U19X_Input DNA


title: HNSC-U19X_H3K4me3_ChIPseq


title: HNSC-U19X_H3K4me1_ChIPseq


title: HNSC-U17B_Input DNA


title: HNSC-U17B_H3K27me3_ChIPseq


title: HNSC-U17B_H3K79me2_ChIPseq


title: HNSC-U22B_H3K4me1_ChIPseq


title: HNSC-U17B_H3K4me3_ChIPseq


title: HNSC-U17B_H3K27ac_ChIPseq


title: HNSC-U17B_H3K9me3_ChIPseq


title: HNSC-U17B_H3K4me1_ChIPseq


title: HNSC-U17A_Input DNA


title: HNSC-U17A_H3K4me3_ChIPseq


title: HNSC-U17A_H3K4me1_ChIPseq


title: HNSC-U14B_H3K27me3_ChIPseq


title: HNSC-U14B_Input DNA


title: HNSC-U17A_H3K27ac_ChIPseq


title: HNSC-U14B_H3K79me2_ChIPseq


title: HNSC-U14B_H3K4me3_ChIPseq


title: HNSC-U14B_H3K27ac_ChIPseq


title: HNSC-U14B_H3K9me3_ChIPseq


title: HNSC-U14B_H3K4me1_ChIPseq


title: HNSC-U14A_Input DNA


title: HNSC-U14A_H3K4me3_ChIPseq


title: HNSC-U11A_H3K4me3_ChIPseq


title: HNSC-U11A_Input DNA


title: HNSC-U11A_H3K4me1_ChIPseq


title: HNSC-U10B_Input DNA


title: HNSC-U10B_H3K4me3_ChIPseq


title: HNSC-U10B_H3K27ac_ChIPseq


title: HNSC-U10A_Input DNA


title: HNSC-U10B_H3K4me1_ChIPseq


title: HNSC-U10B_H3K79me2_ChIPseq


title: HNSC-U10A_H3K4me3_ChIPseq


title: HNSC-U10A_H3K79me2_ChIPseq


title: HNSC-U10A_H3K4me1_ChIPseq


title: HNSC-TR46_H3K4me3_ChIPseq


title: HNSC-TR46_H3K79me2_ChIPseq


title: HNSC-SQCY_H3K27me3_ChIPseq

source_name: HNSC-SQCY

value: HNSC-SQCY


title: HNSC-TR46_Input DNA


title: HNSC-SQCY_H3K4me3_ChIPseq


title: HNSC-SQCY_H3K79me2_ChIPseq


title: HNSC-SQCY_H3K27ac_ChIPseq


title: HNSC-SQCY_H3K9me3_ChIPseq


title: HNSC-SQCY_H3K4me1_ChIPseq


title: HNSC-SC61_H3K27me3_ChIPseq


title: HNSC-SC61_Input DNA


title: HNSC-SC61_H3K4me3_ChIPseq


title: HNSC-SC61_H3K79me2_ChIPseq


title: HNSC-SC61_H3K27ac_ChIPseq


title: HNSC-SC61_H3K9me3_ChIPseq


title: HNSC-PJ34_Input DNA


title: HNSC-PJ34_H3K27me3_ChIPseq


title: HNSC-PJ34_H3K4me3_ChIPseq


title: HNSC-PJ34_H3K27ac_ChIPseq


title: HNSC-PC5B_Input DNA


title: HNSC-PJ34_H3K79me2_ChIPseq


title: HNSC-PJ34_H3K4me1_ChIPseq


title: HNSC-PJ34_H3K9me3_ChIPseq


title: HNSC-PC5B_H3K4me1_ChIPseq


title: HNSC-PC5B_H3K27ac_ChIPseq


title: HNSC-PC5A_H3K4me3_ChIPseq


title: HNSC-PC5A_H3K27ac_ChIPseq


title: HNSC-PC5A_H3K9me3_ChIPseq


title: HNSC-PC5B_H3K4me3_ChIPseq


title: HNSC-PC24_Input DNA


title: HNSC-OS19_Input DNA


title: HNSC-PC5A_H3K4me1_ChIPseq


title: HNSC-PC24_H3K4me3_ChIPseq


title: HNSC-PC5A_Input DNA


title: HNSC-OS19_H3K4me3_ChIPseq


title: HNSC-OS19_H3K79me2_ChIPseq


title: HNSC-OS19_H3K27ac_ChIPseq


title: HNSC-OS19_H3K4me1_ChIPseq


title: HNSC-NOM9_H3K4me3_ChIPseq


title: HNSC-MD8L_Input DNA


title: HNSC-NOM9_H3K27me3_ChIPseq


title: HNSC-MD8L_H3K4me3_ChIPseq


title: HNSC-MD8L_H3K27me3_ChIPseq


title: HNSC-MD8L_H3K27ac_ChIPseq


title: HNSC-MD8L_H3K4me1_ChIPseq


title: HNSC-NOM9_Input DNA


title: HNSC-MD8L_H3K9me3_ChIPseq


title: HNSC-MD1T_Input DNA


title: HNSC-MD1T_H3K27me3_ChIPseq


title: HNSC-MD1T_H3K4me3_ChIPseq


title: HNSC-MD1T_H3K79me2_ChIPseq


title: HNSC-MD1T_H3K27ac_ChIPseq


title: HNSC-MD1T_H3K4me1_ChIPseq


title: HNSC-M68L_Input DNA


title: HNSC-M68L_H3K27me3_ChIPseq


title: HNSC-M68L_H3K4me3_ChIPseq


title: HNSC-M68L_H3K27ac_ChIPseq


title: HNSC-M68L_H3K79me2_ChIPseq


title: HNSC-M68L_H3K9me3_ChIPseq


title: HNSC-M68L_H3K4me1_ChIPseq


title: HNSC-M19L_H3K27me3_ChIPseq


title: HNSC-M19L_H3K4me3_ChIPseq


title: HNSC-M19L_Input DNA


title: HNSC-M19L_H3K79me2_ChIPseq


title: HNSC-M19L_H3K9me3_ChIPseq


title: HNSC-M19L_H3K27ac_ChIPseq


title: HNSC-M19L_H3K4me1_ChIPseq


title: HNSC-M13L_Input DNA


title: HNSC-M13L_H3K27me3_ChIPseq


title: HNSC-M13L_H3K4me3_ChIPseq


title: HNSC-M13L_H3K79me2_ChIPseq


title: HNSC-M13L_H3K27ac_ChIPseq


title: HNSC-M13L_H3K9me3_ChIPseq


title: HNSC-JHU2_Input DNA


title: HNSC-JHU2_H3K4me3_ChIPseq


title: HNSC-JHU2_H3K27ac_ChIPseq


title: HNSC-JHU1_Input DNA


title: HNSC-JHU2_H3K4me1_ChIPseq


title: HNSC-JHU2_H3K79me2_ChIPseq


title: HNSC-JHU1_H3K4me3_ChIPseq


title: HNSC-JHU1_H3K4me1_ChIPseq


title: HNSC-JH22_Input DNA


title: HNSC-JH22_H3K27me3_ChIPseq


title: HNSC-JH22_H3K4me3_ChIPseq


title: HNSC-JH22_H3K27ac_ChIPseq


title: HNSC-JH22_H3K9me3_ChIPseq


title: HNSC-JH22_H3K4me1_ChIPseq


title: HNSC-HN5X_Input DNA


title: HNSC-HN5X_H3K27me3_ChIPseq


title: HNSC-HN5X_H3K27ac_ChIPseq


title: HNSC-HN5X_H3K4me1_ChIPseq


title: HNSC-HN5X_H3K9me3_ChIPseq


title: HNSC-HN5X_H3K4me3_ChIPseq


title: HNSC-HN4X_Input DNA


title: HNSC-HN4X_H3K27me3_ChIPseq


title: HNSC-HN4X_H3K4me3_ChIPseq


title: HNSC-HN4X_H3K27ac_ChIPseq


title: HNSC-HN4X_H3K9me3_ChIPseq


title: HNSC-HN4X_H3K4me1_ChIPseq


title: HNSC-HN31_Input DNA


title: HNSC-HN31_H3K27me3_ChIPseq


title: HNSC-HN31_H3K9me3_ChIPseq


title: HNSC-HN31_H3K27ac_ChIPseq


title: HNSC-HN31_H3K79me2_ChIPseq


title: HNSC-HN31_H3K4me3_ChIPseq


title: HNSC-HN30_H3K79me2_ChIPseq


title: HNSC-HN30_H3K4me3_ChIPseq


title: HNSC-HN30_H3K27ac_ChIPseq


title: HNSC-HN30_Input DNA


title: HNSC-HN31_H3K4me1_ChIPseq


title: HNSC-DETR_Input DNA

source_name: HNSC-DETR

value: HNSC-DETR


title: HNSC-DETR_H3K79me2_ChIPseq


title: HNSC-HN30_H3K4me1_ChIPseq


title: HNSC-DETR_H3K4me3_ChIPseq


title: HNSC-DETR_H3K4me1_ChIPseq


title: HNSC-DETR_H3K27ac_ChIPseq


title: HNSC-CA27_Input DNA


title: HNSC-CA27_H3K27me3_ChIPseq


title: HNSC-CA27_H3K4me3_ChIPseq


title: HNSC-CA27_H3K9me3_ChIPseq


title: HNSC-CA27_H3K4me1_ChIPseq


title: HNSC-686T_Input DNA


title: HNSC-686T_H3K4me3_ChIPseq


title: HNSC-584A_H3K27me3_ChIPseq


title: HNSC-584A_Input DNA


title: HNSC-584A_H3K4me3_ChIPseq


title: HNSC-584A_H3K79me2_ChIPseq


title: HNSC-584A_H3K27ac_ChIPseq


title: HNSC-183X_Input DNA


title: HNSC-183X_H3K79me2_ChIPseq


title: HNSC-183X_H3K4me3_ChIPseq


title: HNSC-183X_H3K4me1_ChIPseq


title: HNSC-1686_Input DNA


title: HNSC-1686_H3K4me3_ChIPseq


title: HNSC-1686_H3K4me1_ChIPseq


title: HNSC-1586_Input DNA


title: HNSC-1483_Input DNA


title: HNSC-1483_H3K4me3_ChIPseq


title: HNSC-1586_H3K79me2_ChIPseq


title: HNSC-1586_H3K4me3_ChIPseq


title: HNSC-1483_H3K4me1_ChIPseq


title: HNSC-1186_Input DNA


title: HNSC-1483_H3K27ac_ChIPseq


title: HNSC-1186_H3K27me3_ChIPseq


title: HNSC-1186_H3K4me3_ChIPseq


title: HNSC-1186_H3K79me2_ChIPseq


title: HNSC-1186_H3K9me3_ChIPseq


title: HNSC-1186_H3K4me1_ChIPseq


title: GBMC-G044_Input DNA

value: GBM cancer cell line


title: GBMC-G044_H3K4me3_ChIPseq


title: GBMC-G044_H3K9me3_ChIPseq


title: GBMC-G044_H3K4me1_ChIPseq


title: GBMC-G033_Input DNA


title: GBMC-G033_H3K4me3_ChIPseq


title: GBMC-G033_H3K27me3_ChIPseq


title: GBMC-G033_H3K27ac_ChIPseq


title: GBMC-G033_H3K9me3_ChIPseq


title: GBMC-G029_Input DNA


title: GBMC-G033_H3K4me1_ChIPseq


title: GBMC-G029_H3K27me3_ChIPseq


title: GBMC-G029_H3K4me3_ChIPseq


title: GBMC-G029_H3K79me2_ChIPseq


title: GBMC-G029_H3K27ac_ChIPseq


title: GBMC-G029_H3K9me3_ChIPseq


title: GBMC-G029_H3K4me1_ChIPseq


title: GBMC-G028_H3K27ac_ChIPseq


title: GBMC-G028_H3K4me1_ChIPseq


title: GBMC-G028_H3K4me3_ChIPseq


title: GBMC-G018_H3K27me3_ChIPseq


title: GBMC-G018_Input DNA


title: GBMC-G018_H3K79me2_ChIPseq


title: GBMC-G018_H3K4me3_ChIPseq


title: tMCAO-3d-2

city: Shanghai

first: Yueman

address: 160 Pujian Rd

institute: Department of Anesthesiology,  Renji Hospital, School of Medicine Shanghai Jiao Tong University, China

description:
Library name: Sample 6
BD Rhapsody

data_processing:
We applied fastp (version 0.24.0) with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data. To quantify the gene expression of the single-cell data, we first constructed a customized reference genome by integrating the exogenous Tdtomato sequence into the mouse genome mm10 (Ensembl annotation version 100), in which the Tdtomato sequence was annotated as “newscount”, and then performed alignment and quantification using STARsolo (version 2.7.11b) against this integrated genome.
Assembly: mm10(Ensembl100)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Brain

extract_protocol:
The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 20 U/mL Papain and 30 U/mL DNase I for 10 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm and 40µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). All libraries were sequenced by DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) on a 150 bp paired-end run.

treatment_protocol: The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing.

value: Brain

value: brain cells


title: GBMC-G018_H3K27ac_ChIPseq

city: Houston


title: tMCAO-3d-1

description:
Library name: Sample 5
BD Rhapsody


title: tMCAO-1d-2

description:
Library name: Sample 4
BD Rhapsody


title: GBMC-G018_H3K9me3_ChIPseq


title: HNSC-1686_H3K27ac_ChIPseq


title: GBMC-G018_H3K4me1_ChIPseq


title: tMCAO-1d-1

description:
Library name: Sample 3
BD Rhapsody


title: HNSC-1483_H3K79me2_ChIPseq


title: Sham-2

description:
Library name: Sample 2
BD Rhapsody

value: Sham


title: GBMC-G017_Input DNA


title: Sham-1

description:
Library name: Sample 1
BD Rhapsody


title: GBMC-G017_H3K27me3_ChIPseq


title: GBMC-G017_H3K4me3_ChIPseq


title: Ms4a3-cko-2

description:
Library name: Sample 4
BD Rhapsody

data_processing:
We applied fastp (version 0.24.0) with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data.STARSolo was utilized to calculate the raw counts and cell whitelist by default parameter
Assembly: mm10(Ensembl100)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes


title: GBMC-G017_H3K79me2_ChIPseq


title: GBMC-G044_H3K79me2_ChIPseq


title: Ms4a3-cko-1

description:
Library name: Sample 3
BD Rhapsody


title: GBMC-G044_H3K27me3_ChIPseq


title: GBMC-G017_H3K27ac_ChIPseq


title: GBMC-G044_H3K27ac_ChIPseq


title: GBMC-G017_H3K9me3_ChIPseq


title: Flox-2

description:
Library name: Sample 2
BD Rhapsody


title: Flox-1

description:
Library name: Sample 1
BD Rhapsody


title: GBMC-G017_H3K4me1_ChIPseq


title: 8h gladiolin replicate 2

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description:
Library name: Sample 12
W_T_8h_R2

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3' UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Assembly: C. albicans SC5314
Supplementary files format and content: counts.csv is a comma-separated values file containing the raw genetic annotation read count for all samples

organism: Candida albicans

growth_protocol: Wild-type C. albicans cultures were grown on YPD plates (1% yeast extract, 2% peptone, 2% glucose, and 2% agar, 80μg/ml uridine) and hyphal formation induced in MOPS buffered RPMI (Sigma R6504) adjusted to pH 7.0 at 37 °C. Lactate was used at 0.2% (w/v) in RPMI.

extract_protocol:
RNA was extracted using the hot phenol method.
Library construction was by the PAT-seq approach (Harrison et al RNA 2015).

treatment_protocol: Overnight cultures were washed with PBS and diluted to an OD 600  of 0.1 in 4ml RPMI with  16 µg/ml gladiolin or 0.08% DMSO control. Cultures were grown for 1h, 3h or 8h at 37°C, shaking at 200rpm.

value: WT

value: gladiolin

tag: treatment timepoint

value: 8h gladiolin


title: GBMC-G033_H3K79me2_ChIPseq


title: 8h gladiolin replicate 1

description:
Library name: Sample 11
W_T_8h_R1


title: GBMC-G010_Input DNA


title: GBMC-G010_H3K4me3_ChIPseq


title: GBMC-G010_H3K27me3_ChIPseq


title: GBMC-G010_H3K27ac_ChIPseq


title: 8h control replicate 2

description:
Library name: Sample 10
W_C_8h_R2

value: DMSO

value: 8h control


title: 8h control replicate 1

description:
Library name: Sample 9
W_C_8h_R1


title: GBMC-G010_H3K4me1_ChIPseq


title: 3h gladiolin replicate 2

description:
Library name: Sample 8
W_T_3h_R2

value: 3h gladiolin


title: 3h gladiolin replicate 1

description:
Library name: Sample 7
W_T_3h_R1


title: GBMC-G008_Input DNA


title: 3h control replicate 2

description:
Library name: Sample 6
W_C_3h_R2

value: 3h control


title: GBMC-G008_H3K27me3_ChIPseq


title: 3h control replicate 1

description:
Library name: Sample 5
W_C_3h_R1


title: 1h gladiolin replicate 2

description:
Library name: Sample 4
W_T_1h_R2

value: 1h gladiolin


title: GBMC-G008_H3K4me3_ChIPseq