title: Hypothalamus_CUT&Tag_H3K27ac_biological_replicate_3

first: Yifei

last: Zang

address: 2005 Songhu Road

department: School of Life Sciences

description:
Library name: Sample17
HP_H3K27ac_overlap_optimal_peak.narrowPeak

data_processing:
H3K27ac CUT&Tag data were processed using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters. Peak calling was performed with MACS2 using a p-value threshold of 0.01. Peaks consistent between two pseudoreplicates—generated by subsampling pooled reads from all biological replicates—were retained for downstream analysis.
Supplementary files format and content: bigWig, narrowPeak
[Paired-Tag] Paired-tag data were processed using easyPairedTag (https://github.com/YuLab-FDU/easyPairedTag). Briefly, cellular barcodes were extracted using UMI-tools v1.1.4, and adapter sequences as well as low-quality bases were removed with Cutadapt v4.5. Cleaned reads were aligned to the mm10 reference genome using STAR v2.7.10a in single-end mode for RNA and BWA-MEM v0.7.17 in paired-end mode for DNA. Mapped DNA reads were filtered using a MAPQ threshold of >10, and duplicates were removed based on mapped position, cellular barcode, and UMI. RNA alignment files were converted into a matrix with genes as rows and cells as columns. DNA alignment files were converted into a matrix with 5-kb genomic bins as rows and cells as columns. Filtered count matrices from all DNA and RNA sub-libraries were merged to generate a single DNA matrix and a single RNA matrix. Prior to clustering, nuclei with abnormally high or low UMI counts were excluded. Potential doublets were detected and removed from the RNA matrix using Scrublet v0.2.3, and the corresponding DNA barcodes were also excluded.
[CUT&Tag ]  H3K27ac CUT&Tag data were processed using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters. Peak calling was performed with MACS2 using a p-value threshold of 0.01. Peaks consistent between two pseudoreplicates—generated by subsampling pooled reads from all biological replicates—were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: [Paired-Tag] Tab-separated values files and matrix files
Supplementary files format and content: [CUT&Tag ]  bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: hypothalamus

extract_protocol:
Hypothalamic samples were dissected and finely minced on ice. The tissue fragments were lysed in cold nuclear extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine (Sigma-Aldrich, 05292), and 1× cOmplete™ Mini EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001)) for 10 minutes. After centrifugation at 500 rpm for 10 minutes at 4 °C, the supernatant was carefully removed, and the nuclei were resuspended in PBS supplemented with 1% BSA.
CUT&Tag was performed using a modified protocol. Nuclei were first incubated in cold antibody buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01%IGEPAL-CA630, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2 mM EDTA) containing anti-H3K27ac antibody (Abcam, ab7429) and pA-Tn5. The suspension was rotated for 1 hour and then incubated overnight at 4 °C. Following incubation, nuclei were washed twice with Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01% digitonin), then incubated in tagmentation buffer (Digitonin300 buffer supplemented with 10 mM MgCl₂) for 1 hour at 37 °C. To terminate tagmentation and release DNA fragments, nuclei were lysed in lysis buffer (10 mM EDTA, 0.1% SDS, 20 mg/mL Proteinase K) and incubated for 1 hour at 50 °C. DNA was purified by phenol-chloroform extraction. Libraries were amplified with 6 PCR cycles and purified using 0.8× AMPure XP beads (Beckman Coulter, A63881). Sequencing was performed on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.
[Paired-Tag] Single-cell suspension were prepared from hypothalamus tissues in douncing buffer with Protease/RNase Inhibitor cocktail (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1X Protease Inhibitor, 0.5 U/µL RNase OUT, 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X100 (Sigma T9284). The cell suspension was then through a 30 µm Cell-Tric (Sysmex) and centrifuged at 1,000 g for 10 min, 4 °C. Cell pellets were washed with fresh douncing buffer, centrifuged again, and then resuspended in NIB containing 0.2% IGEPAL CA-630. The suspension was rotated for 10 minutes at 4 °C to lyse the cells and release nuclei. Nuclei were counted using a Bio-Rad TC20™ cell counter and immediately processed for Paired-Tag experiments.
[Paired-Tag] Libraries were prepared using the Paired-tag workflow. Briefly, permeabilized nuclei were first incubated with antibodies targeting specific chromatin regions to enable the binding of protein A-fused Tn5 transposase. Tagmentation and reverse transcription were then performed sequentially. Specifically, reactions were carried out in 12 wells, each using the paired set of barcodes incorporated into the transposase adaptors and reverse transcription (RT) primers, thereby labeling different samples with the first round of barcodes. Next, a ligation-based combinatorial barcoding strategy was employed to introduce the second and third rounds of barcodes. This was achieved by sequentially ligating well-specific DNA barcodes—derived from 96-well plates—to the 5’ ends of both DNA fragments and cDNA. Finally, the barcoded nuclei were divided into sub-libraries and lysed, after which DNA and cDNA were purified, amplified, and split into two separate sequencing libraries.
[CUT&Tag ]  Hypothalamic samples were dissected and finely minced on ice. The tissue fragments were lysed in cold nuclear extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine (Sigma-Aldrich, 05292), and 1× cOmplete™ Mini EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001)) for 10 minutes. After centrifugation at 500 rpm for 10 minutes at 4 °C, the supernatant was carefully removed, and the nuclei were resuspended in PBS supplemented with 1% BSA.
[CUT&Tag ] CUT&Tag was performed using a modified protocol. Nuclei were first incubated in cold antibody buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01%IGEPAL-CA630, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2 mM EDTA) containing anti-H3K27ac antibody (Abcam, ab7429) and pA-Tn5. The suspension was rotated for 1 hour and then incubated overnight at 4 °C. Following incubation, nuclei were washed twice with Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01% digitonin), then incubated in tagmentation buffer (Digitonin300 buffer supplemented with 10 mM MgCl₂) for 1 hour at 37 °C. To terminate tagmentation and release DNA fragments, nuclei were lysed in lysis buffer (10 mM EDTA, 0.1% SDS, 20 mg/mL Proteinase K) and incubated for 1 hour at 50 °C. DNA was purified by phenol-chloroform extraction. Libraries were amplified with 6 PCR cycles and purified using 0.8× AMPure XP beads (Beckman Coulter, A63881). Sequencing was performed on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.

value: hypothalamus

tag: chip antibody

value: H3K27ac (Abcam, ab7429)


title: N2_5_CAM787_4

status: Public on Aug 31 2025

type: SRA

city: Haifa

first: Nabeel

middle: S.

last: Ganem

address: Stern lab, Faculty of Biology, Technion City, Haifa 3200003, Israel.

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: Library name: N2_5_CAM787_4

library_source: transcriptomic

data_processing:
Data was generated using Illumina NextSeq platforms: either NextSeq 550 with the High Output Kit v2.5 (75 cycles) or NextSeq 2000 with the P2 100 cycles kit, both with sequencing parameters of Read1-36, Index1-8, Index2-8, and Read2-37.
Assembly: The obtained sequencing read fragments were aligned to the WBPS16 using the STAR aligner  (Dobin et al., 2013) v2.7.9a. Expression levels of single gene were normalized by gene mapped counts per million total reads (RPM).
Supplementary files format and content: text  files for both strains including all samples and time for each sample and RPM value for each gene

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Single individual

growth_protocol: C. elegans woms (wild-type N2 and tph-1 mutant) were cultured on NGM agar with OP50 E. coli following standard protocols (Brenner, 1974). For behavioral imaging, eggs obtained by bleaching were placed individually in 10 mm circular arenas on custom multi-well plates containing NGM agar with UV-killed OP50 to prevent bacterial growth during experiments (Stern et al., 2017).

extract_protocol:
Fresh working lysis buffer is prepared daily by mixing a stable lysis buffer stock (made of Tris-HCl, Triton-X, Tween-20, EDTA, and water), Proteinase K, and RNase inhibitor. Worms were collected individually, and cut with a needle if larval. After adding lysis buffer, samples are mixed, centrifuged, and incubated in a thermocycler at 65 °C for 10 min, 85 °C for 1 min, then 4 °C before cooling on ice.
Library preparation for each single individual was according to the Illumina Nextera tagmentation protocol (Illumina), with DNA input and reagents adjusted for 20 ng of cDNA. The tagmented DNA was cleaned, and PCR amplification was performed. PCR primers were removed using Ampure XP beads.

treatment_protocol: After the behavioral experiment, each individual was pipetted in 2 μl UltraPure  water onto the side wall of a 0.2 ml PCR tube containing 2 μl Lysis buffer. The tube was laid on its side under a ZEISS Stemi 508 dissecting microscope, and the worm was cut into several fragments with a sterile 25 G 1.5-inch needle, spun down, shock-frozen in liquid nitrogen, and stored at −80 °C until use

tag: tissue

value: Single individual

tag: developmental stage

tag: strain

tag: genotype

value: WT

tag: time (min_in_l4_stage)


title: Hippocampus, 3 Months, Rep7

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

country: Germany

institute: Christian-Albrechts-University Kiel

description:
Library name: 3M.N7
3M_6, J14270

library_source: genomic

data_processing:
Sequence information was converted to fastq format using bcl2fastq v2.20.0.422. From validation samples only those reads were downstream processed, that start with a Tecan/NuGen TrueMethyl diversity adapter (length 0-3, clipped afterwards) followed by a MspI cutting site.
Read quality trimming (cutoff 20) and TruSeq universal adapter clipping was performed using Cutadapt v2.10. Due to MspI cutting site end-repair, R1 adapter was prefixed by NN and in case of paired-end data, unconditional 5' clipping of length 2 was conducted on R2.
Mappings were done via segemehl v0.3.4 (methyl-C mode, accuracy 95%, reference GRCm38) and filtered for unique alignments. Paired-end alignments were further filtered for proper-read pairs and overlaps of R2 with R1 were trimmed using BamUtil clipOverlap v1.0.14.
Validation data alignments were deduplicated for over amplified PCR fragments based on unique molecular identifiers utilizing UMI-tools v1.1.1.
Methylation rates were inferred utilizing haarz v0.3.0. Rates and coverages within a CpG context were compiled using BEDTools v2.30.0.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tabular delimited text file in bismark cov format of methylated and unmethylated CpG coverage per GRCm38 chromosomal CpG and sample.

molecule: genomic DNA

organism: Mus musculus

source_name: Hippocampus

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen).
200 ng of DNA was fragmented via a 5 hour Msp1-digest (New England Biolabs), followed by TrueSeq adapter ligation (Illumina, San Diego, CA, USA) and subsequent bisulfite conversion following the manufacturers protocol (EZ DNA Methylation Gold Kit, Zymo Research). The bisulfite converted DNA was amplified in a 19-cycles PCR with Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies) and the resulting libraries were quality checked using 4200 TapeStation (Agilent Technologies). For sequencing of validation samples, Illumina’s next-generation sequencing methodology 87 was used. In detail, genomic DNA was quality checked and quantified using the 4200 TapeStation instruments in combination with the Genomic DNA ScreenTape (both Agilent Technologies). Libraries were prepared from 100 ng of input material using Ovation RRBS Methyl-Seq with TrueMethyl oxBS (Tecan). In detail, only the bisulfite part of the protocol was followed, oxidation of DNA was not done, and samples were treated as MOCK oxBS samples according to the manufacturer’s instruction. Quantification and quality check of libraries were done using the 4200 TapeStation and D5000 ScreenTapes instruments (both Agilent Technologies).

value: Hippocampus

tag: Sex

value: Male

tag: age

value: 3 Months


title: 7-C01D01

city: PHOENIX

first: Aarthi

last: Talla

state: ARIZONA

address: 2448 W ROWEL RD

country: USA

institute: IMMUNASYST

description:
Library name: Sample 41
whole blood collected from timepoint C01D01

data_processing:
Samples were demutliplexed using 'bcl2fastq.1.8.4' (*Note - Raw Fastqs for some samples are unavailable since they were lost during lab relocation).
The sequencing raw reads were trimmed off adapter sequence contaminants using Trimmomatic 0.32.
The trimmed reads mapped onto the Ensembl version of the human genome (Ensembl - Grch38), using the STAR 2.4.0f1 aligner.
The transcript abundance was then estimated by counting the number of reads mapping to the exons that are unique to the transcripts of a gene using HTSeq. The obtained transcript counts were normalized by TMM (Trimmed Mean of M-values) by correcting for the library size and differential expressed genes were determined using the edgeR Bioconductor package.
Whole blood RNA-sequencing was done in 2 batches and transcript count matrices were corrected using the ComBat package in R.
Assembly: Ensembl - Grch38
Supplementary files format and content: Tab delimited text files of the batch corrected counts per million (CPM) of every transcript per sample are provided.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
10mL of whole peripheral blood (collected in PAXgene tubes) were collected for each sample and cryopreserved at -80C. The PreAnalytix PAXgene Blood RNA  kit was used to extract RNA and an RNA-integrity number of 8 or above (measured using a bioanalyzer) was ensured prior to library preparation.
The construction of mRNA libraries was performed according to the Illumina TruSeq V2 library preparation kit. The validation of these libraries occurred through microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantification using Kapa Library Quantification Kits (Roche), and eventual pooling and clustering on Illumina TruSeq V2 flow cells.

tag: cell type

value: whole blood

tag: disease state

value: HIV infected

tag: time

tag: treatment

value: pre-treatment/baseline

tag: participant id


title: 4-C01D02

description:
Library name: Sample 35
whole blood collected from timepoint C01D02


title: N2_1_CAM795_3

description: Library name: N2_1_CAM795_3


title: Hypothalamus_CUT&Tag_H3K27ac_biological_replicate_1

city: Shanghai

country: China

institute: Fudan University

description:
Library name: Sample15
HP_H3K27ac_overlap_optimal_peak.narrowPeak

data_processing:
[Paired-Tag] Paired-tag data were processed using easyPairedTag (https://github.com/YuLab-FDU/easyPairedTag). Briefly, cellular barcodes were extracted using UMI-tools v1.1.4, and adapter sequences as well as low-quality bases were removed with Cutadapt v4.5. Cleaned reads were aligned to the mm10 reference genome using STAR v2.7.10a in single-end mode for RNA and BWA-MEM v0.7.17 in paired-end mode for DNA. Mapped DNA reads were filtered using a MAPQ threshold of >10, and duplicates were removed based on mapped position, cellular barcode, and UMI. RNA alignment files were converted into a matrix with genes as rows and cells as columns. DNA alignment files were converted into a matrix with 5-kb genomic bins as rows and cells as columns. Filtered count matrices from all DNA and RNA sub-libraries were merged to generate a single DNA matrix and a single RNA matrix. Prior to clustering, nuclei with abnormally high or low UMI counts were excluded. Potential doublets were detected and removed from the RNA matrix using Scrublet v0.2.3, and the corresponding DNA barcodes were also excluded.
[CUT&Tag ]  H3K27ac CUT&Tag data were processed using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters. Peak calling was performed with MACS2 using a p-value threshold of 0.01. Peaks consistent between two pseudoreplicates—generated by subsampling pooled reads from all biological replicates—were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: [Paired-Tag] Tab-separated values files and matrix files
Supplementary files format and content: [CUT&Tag ]  bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
[Paired-Tag] Single-cell suspension were prepared from hypothalamus tissues in douncing buffer with Protease/RNase Inhibitor cocktail (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1X Protease Inhibitor, 0.5 U/µL RNase OUT, 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X100 (Sigma T9284). The cell suspension was then through a 30 µm Cell-Tric (Sysmex) and centrifuged at 1,000 g for 10 min, 4 °C. Cell pellets were washed with fresh douncing buffer, centrifuged again, and then resuspended in NIB containing 0.2% IGEPAL CA-630. The suspension was rotated for 10 minutes at 4 °C to lyse the cells and release nuclei. Nuclei were counted using a Bio-Rad TC20™ cell counter and immediately processed for Paired-Tag experiments.
[Paired-Tag] Libraries were prepared using the Paired-tag workflow. Briefly, permeabilized nuclei were first incubated with antibodies targeting specific chromatin regions to enable the binding of protein A-fused Tn5 transposase. Tagmentation and reverse transcription were then performed sequentially. Specifically, reactions were carried out in 12 wells, each using the paired set of barcodes incorporated into the transposase adaptors and reverse transcription (RT) primers, thereby labeling different samples with the first round of barcodes. Next, a ligation-based combinatorial barcoding strategy was employed to introduce the second and third rounds of barcodes. This was achieved by sequentially ligating well-specific DNA barcodes—derived from 96-well plates—to the 5’ ends of both DNA fragments and cDNA. Finally, the barcoded nuclei were divided into sub-libraries and lysed, after which DNA and cDNA were purified, amplified, and split into two separate sequencing libraries.
[CUT&Tag ]  Hypothalamic samples were dissected and finely minced on ice. The tissue fragments were lysed in cold nuclear extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine (Sigma-Aldrich, 05292), and 1× cOmplete™ Mini EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001)) for 10 minutes. After centrifugation at 500 rpm for 10 minutes at 4 °C, the supernatant was carefully removed, and the nuclei were resuspended in PBS supplemented with 1% BSA.
[CUT&Tag ] CUT&Tag was performed using a modified protocol. Nuclei were first incubated in cold antibody buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01%IGEPAL-CA630, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2 mM EDTA) containing anti-H3K27ac antibody (Abcam, ab7429) and pA-Tn5. The suspension was rotated for 1 hour and then incubated overnight at 4 °C. Following incubation, nuclei were washed twice with Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01% digitonin), then incubated in tagmentation buffer (Digitonin300 buffer supplemented with 10 mM MgCl₂) for 1 hour at 37 °C. To terminate tagmentation and release DNA fragments, nuclei were lysed in lysis buffer (10 mM EDTA, 0.1% SDS, 20 mg/mL Proteinase K) and incubated for 1 hour at 50 °C. DNA was purified by phenol-chloroform extraction. Libraries were amplified with 6 PCR cycles and purified using 0.8× AMPure XP beads (Beckman Coulter, A63881). Sequencing was performed on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.


title: 3-C01D01

description:
Library name: Sample 32
whole blood collected from timepoint C01D01


title: 3-C01D02

description:
Library name: Sample 33
whole blood collected from timepoint C01D02


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#07

description:
Library name: Sample14
Paired-tag_RNA_filtered_matrix.tar.gz

data_processing:
[Paired-Tag] Paired-tag data were processed using easyPairedTag (https://github.com/YuLab-FDU/easyPairedTag). Briefly, cellular barcodes were extracted using UMI-tools v1.1.4, and adapter sequences as well as low-quality bases were removed with Cutadapt v4.5. Cleaned reads were aligned to the mm10 reference genome using STAR v2.7.10a in single-end mode for RNA and BWA-MEM v0.7.17 in paired-end mode for DNA. Mapped DNA reads were filtered using a MAPQ threshold of >10, and duplicates were removed based on mapped position, cellular barcode, and UMI. RNA alignment files were converted into a matrix with genes as rows and cells as columns. DNA alignment files were converted into a matrix with 5-kb genomic bins as rows and cells as columns. Filtered count matrices from all DNA and RNA sub-libraries were merged to generate a single DNA matrix and a single RNA matrix. Prior to clustering, nuclei with abnormally high or low UMI counts were excluded. Potential doublets were detected and removed from the RNA matrix using Scrublet v0.2.3, and the corresponding DNA barcodes were also excluded.
[CUT&Tag ]  H3K27ac CUT&Tag data were processed using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters. Peak calling was performed with MACS2 using a p-value threshold of 0.01. Peaks consistent between two pseudoreplicates—generated by subsampling pooled reads from all biological replicates—were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: [Paired-Tag] Tab-separated values files and matrix files
Supplementary files format and content: [CUT&Tag ]  bigWig, narrowPeak

molecule: nuclear RNA

value: H3K27ac (Abcam, ab7429) and H3K27me3 (Activate motif, 39155)


title: 6-C01D02

description:
Library name: Sample 40
whole blood collected from timepoint C01D02


title: N2_3_CAM796_6

description: Library name: N2_3_CAM796_6


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#07

description:
Library name: Sample13
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz


title: N2_4_CAM040_1

description: Library name: N2_4_CAM040_1


title: N2_1_CAM788_5

description: Library name: N2_1_CAM788_5


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#06

description:
Library name: Sample12
Paired-tag_RNA_filtered_matrix.tar.gz


title: 22-C01D02

description:
Library name: Sample 31
whole blood collected from timepoint C01D02


title: N2_2_CAM791_2

description: Library name: N2_2_CAM791_2


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#06

description:
Library name: Sample11
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz


title: 20-C01D02

description:
Library name: Sample 29
whole blood collected from timepoint C01D02


title: Hypothalamus_CUT&Tag_H3K27ac_biological_replicate_2

description:
Library name: Sample16
HP_H3K27ac_overlap_optimal_peak.narrowPeak


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#05

description:
Library name: Sample9
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz


title: 2-EOT

description:
Library name: Sample 27
whole blood collected from timepoint EOT

value: EOT


title: 4-C01D01

description:
Library name: Sample 34
whole blood collected from timepoint C01D01


title: N2_2_CAM791_4

description: Library name: N2_2_CAM791_4


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#04

description:
Library name: Sample8
Paired-tag_RNA_filtered_matrix.tar.gz


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#04

description:
Library name: Sample7
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz


title: N2_5_CAM788_4

description: Library name: N2_5_CAM788_4


title: 2-C01D01

description:
Library name: Sample 25
whole blood collected from timepoint C01D01


title: N2_3_CAM787_4

description: Library name: N2_3_CAM787_4


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#05

description:
Library name: Sample10
Paired-tag_RNA_filtered_matrix.tar.gz


title: N2_1_CAM787_5

description: Library name: N2_1_CAM787_5


title: 19-C01D01

description:
Library name: Sample 23
whole blood collected from timepoint C01D01


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#03

description:
Library name: Sample5
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz


title: N2_5_CAM795_1

description: Library name: N2_5_CAM795_1


title: 22-C01D01

description:
Library name: Sample 30
whole blood collected from timepoint C01D01


title: 17-C01D02

description:
Library name: Sample 22
whole blood collected from timepoint C01D02


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#02

description:
Library name: Sample3
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz


title: N2_2_CAM787_5

description: Library name: N2_2_CAM787_5


title: N2_1_CAM787_1

description: Library name: N2_1_CAM787_1


title: 2-C01D02

description:
Library name: Sample 26
whole blood collected from timepoint C01D02


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#01

description:
Library name: Sample2
Paired-tag_RNA_filtered_matrix.tar.gz


title: 20-C01D01

description:
Library name: Sample 28
whole blood collected from timepoint C01D01


title: N2_5_CAM787_5

description: Library name: N2_5_CAM787_5


title: 16-C01D02

description:
Library name: Sample 20
whole blood collected from timepoint C01D02


title: N2_2_CAM796_6

description: Library name: N2_2_CAM796_6


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#03

description:
Library name: Sample6
Paired-tag_RNA_filtered_matrix.tar.gz


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_DNA#01

description:
Library name: Sample1
Paired-tag_H3K27ac_filtered_matrix.tar.gz
Paired-tag_H3K27me3_filtered_matrix.tar.gz

data_processing:
[CUT&Tag ]  H3K27ac CUT&Tag data were processed using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters. Peak calling was performed with MACS2 using a p-value threshold of 0.01. Peaks consistent between two pseudoreplicates—generated by subsampling pooled reads from all biological replicates—were retained for downstream analysis.
Supplementary files format and content: [CUT&Tag ]  bigWig, narrowPeak
[Paired-Tag] Paired-tag data were processed using easyPairedTag (https://github.com/YuLab-FDU/easyPairedTag). Briefly, cellular barcodes were extracted using UMI-tools v1.1.4, and adapter sequences as well as low-quality bases were removed with Cutadapt v4.5. Cleaned reads were aligned to the mm10 reference genome using STAR v2.7.10a in single-end mode for RNA and BWA-MEM v0.7.17 in paired-end mode for DNA. Mapped DNA reads were filtered using a MAPQ threshold of >10, and duplicates were removed based on mapped position, cellular barcode, and UMI. RNA alignment files were converted into a matrix with genes as rows and cells as columns. DNA alignment files were converted into a matrix with 5-kb genomic bins as rows and cells as columns. Filtered count matrices from all DNA and RNA sub-libraries were merged to generate a single DNA matrix and a single RNA matrix. Prior to clustering, nuclei with abnormally high or low UMI counts were excluded. Potential doublets were detected and removed from the RNA matrix using Scrublet v0.2.3, and the corresponding DNA barcodes were also excluded.
[CUT&Tag ]  H3K27ac CUT&Tag data were processed using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters. Peak calling was performed with MACS2 using a p-value threshold of 0.01. Peaks consistent between two pseudoreplicates—generated by subsampling pooled reads from all biological replicates—were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: [Paired-Tag] Tab-separated values files and matrix files
Supplementary files format and content: [CUT&Tag ]  bigWig, narrowPeak

extract_protocol:
[CUT&Tag ]  Hypothalamic samples were dissected and finely minced on ice. The tissue fragments were lysed in cold nuclear extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine (Sigma-Aldrich, 05292), and 1× cOmplete™ Mini EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001)) for 10 minutes. After centrifugation at 500 rpm for 10 minutes at 4 °C, the supernatant was carefully removed, and the nuclei were resuspended in PBS supplemented with 1% BSA.
[CUT&Tag ] CUT&Tag was performed using a modified protocol. Nuclei were first incubated in cold antibody buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01%IGEPAL-CA630, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2 mM EDTA) containing anti-H3K27ac antibody (Abcam, ab7429) and pA-Tn5. The suspension was rotated for 1 hour and then incubated overnight at 4 °C. Following incubation, nuclei were washed twice with Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01% digitonin), then incubated in tagmentation buffer (Digitonin300 buffer supplemented with 10 mM MgCl₂) for 1 hour at 37 °C. To terminate tagmentation and release DNA fragments, nuclei were lysed in lysis buffer (10 mM EDTA, 0.1% SDS, 20 mg/mL Proteinase K) and incubated for 1 hour at 50 °C. DNA was purified by phenol-chloroform extraction. Libraries were amplified with 6 PCR cycles and purified using 0.8× AMPure XP beads (Beckman Coulter, A63881). Sequencing was performed on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.
[Paired-Tag] Single-cell suspension were prepared from hypothalamus tissues in douncing buffer with Protease/RNase Inhibitor cocktail (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1X Protease Inhibitor, 0.5 U/µL RNase OUT, 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X100 (Sigma T9284). The cell suspension was then through a 30 µm Cell-Tric (Sysmex) and centrifuged at 1,000 g for 10 min, 4 °C. Cell pellets were washed with fresh douncing buffer, centrifuged again, and then resuspended in NIB containing 0.2% IGEPAL CA-630. The suspension was rotated for 10 minutes at 4 °C to lyse the cells and release nuclei. Nuclei were counted using a Bio-Rad TC20™ cell counter and immediately processed for Paired-Tag experiments.
[Paired-Tag] Libraries were prepared using the Paired-tag workflow. Briefly, permeabilized nuclei were first incubated with antibodies targeting specific chromatin regions to enable the binding of protein A-fused Tn5 transposase. Tagmentation and reverse transcription were then performed sequentially. Specifically, reactions were carried out in 12 wells, each using the paired set of barcodes incorporated into the transposase adaptors and reverse transcription (RT) primers, thereby labeling different samples with the first round of barcodes. Next, a ligation-based combinatorial barcoding strategy was employed to introduce the second and third rounds of barcodes. This was achieved by sequentially ligating well-specific DNA barcodes—derived from 96-well plates—to the 5’ ends of both DNA fragments and cDNA. Finally, the barcoded nuclei were divided into sub-libraries and lysed, after which DNA and cDNA were purified, amplified, and split into two separate sequencing libraries.
[CUT&Tag ]  Hypothalamic samples were dissected and finely minced on ice. The tissue fragments were lysed in cold nuclear extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine (Sigma-Aldrich, 05292), and 1× cOmplete™ Mini EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001)) for 10 minutes. After centrifugation at 500 rpm for 10 minutes at 4 °C, the supernatant was carefully removed, and the nuclei were resuspended in PBS supplemented with 1% BSA.
[CUT&Tag ] CUT&Tag was performed using a modified protocol. Nuclei were first incubated in cold antibody buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01%IGEPAL-CA630, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2 mM EDTA) containing anti-H3K27ac antibody (Abcam, ab7429) and pA-Tn5. The suspension was rotated for 1 hour and then incubated overnight at 4 °C. Following incubation, nuclei were washed twice with Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× cOmplete™ Mini EDTA-free protease inhibitor, 0.01% digitonin), then incubated in tagmentation buffer (Digitonin300 buffer supplemented with 10 mM MgCl₂) for 1 hour at 37 °C. To terminate tagmentation and release DNA fragments, nuclei were lysed in lysis buffer (10 mM EDTA, 0.1% SDS, 20 mg/mL Proteinase K) and incubated for 1 hour at 50 °C. DNA was purified by phenol-chloroform extraction. Libraries were amplified with 6 PCR cycles and purified using 0.8× AMPure XP beads (Beckman Coulter, A63881). Sequencing was performed on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.


title: N2_2_CAM787_4

description: Library name: N2_2_CAM787_4


title: 16-C01D01

description:
Library name: Sample 19
whole blood collected from timepoint C01D01


title: N2_1_CAM796_5

description: Library name: N2_1_CAM796_5


title: 19-C01D02

description:
Library name: Sample 24
whole blood collected from timepoint C01D02


title: Tumor, MC38, p53 KO, anti-PD-1, TCR

city: Pittsburgh

first: David

middle: Shihong

last: Gao

state: PA

address: 5051 Centre Avenue

department: Immunology

institute: University of Pittsburgh

description:
Library name: KO_TCR
C57BL/6J mice

data_processing:
Raw data were processed by cellranger 6.1.1
Assembly: mm10
Supplementary files format and content: Standard single cell format

source_name: Tumor

growth_protocol: MC38 cell lines were grown in DMEM with 10% FBS and 1% P.S.

extract_protocol:
10x single cell chromium
5' GEX along with TCR libraries

value: Tumor

tag: cell line

value: Whole tumor

value: p53 KO


title: Tumor, MC38, WT, anti-PD-1, TCR

description:
Library name: Control_TCR
C57BL/6J mice


title: Tumor, MC38, p53 KO, anti-PD-1, GEX

description:
Library name: KO_GEX
C57BL/6J mice

library_source: transcriptomic single cell


title: 15-C01D01

description:
Library name: Sample 16
whole blood collected from timepoint C01D01


title: N2_5_CAM791_3

description: Library name: N2_5_CAM791_3


title: 17-C01D01

description:
Library name: Sample 21
whole blood collected from timepoint C01D01


title: N2_1_CAM788_6

description: Library name: N2_1_CAM788_6


title: Tumor, MC38, WT, anti-PD-1, GEX

description:
Library name: Control_GEX
C57BL/6J mice


title: N2_2_CAM040_2

description: Library name: N2_2_CAM040_2


title: 13-EOT

description:
Library name: Sample 12
whole blood collected from timepoint EOT


title: SKO_25B5

city: Ottawa

first: Vern

last: Lewis

state: Ontario

address: 1125 Colonel By Drive

department: Neuroscience

country: Canada

institute: Carleton University

description: Library name: SKO_Veh_6

data_processing:
Quality control & trimming: FastP & FastQC
Analysis pipeline: STAR (v.2.7.11b) -> FeatureCounts (v.2.0.8) -> DESeq2
RPKM conversion:  edgeR’s RPKM function
Assembly: Mouse genome: GRCm39
Supplementary files format and content: Matrix of read counts (TPM)

source_name: hippocampal tissue

extract_protocol:
Trizol exraction & Rnease minikit (Qiagen)
*Prepared by sequenciung facility

treatment_protocol: Male or female mice of three different genotypes (Wildtype, Fmr1, or Shank3 KO). Within each of these sexes and genotypes, mice were given subcutaneous injecitons of either cannabidiol (CBD) (5mg/kg for males and 50mg/kg for females) or vehicle for 7 days.

value: hippocampal tissue

value: Sko-/-

value: Veh


title: N2_2_CAM795_5

description: Library name: N2_2_CAM795_5


title: SKO_25B2

description: Library name: SKO_Veh_5

value: veh


title: 14-C01D01

description:
Library name: Sample 13
whole blood collected from timepoint C01D01


title: SKO_24B3

description: Library name: SKO_CBD_5

value: CBD


title: Hypothalamus_Paired-Tag_H3K27ac_H3K27me3_sub_library_RNA#02

description:
Library name: Sample4
Paired-tag_RNA_filtered_matrix.tar.gz

value: hypothalamus


title: 13-C01D02

description:
Library name: Sample 11
whole blood collected from timepoint C01D02


title: 15-EOT

description:
Library name: Sample 18
whole blood collected from timepoint EOT


title: N2_1_CAM795_1

description: Library name: N2_1_CAM795_1

value: Single individual

value: WT


title: SKO_24A5

description: Library name: SKO_CBD_4


title: 15-C01D02

description:
Library name: Sample 17
whole blood collected from timepoint C01D02


title: 14-EOT

description:
Library name: Sample 15
whole blood collected from timepoint EOT


title: SKO_26C2

description: Library name: SKO_CBD_6


title: N2_3_CAM040_6

description: Library name: N2_3_CAM040_6


title: SKO_24A4

description: Library name: SKO_Veh_4


title: 13-C01D01

description:
Library name: Sample 10
whole blood collected from timepoint C01D01


title: N2_2_CAM040_5

description: Library name: N2_2_CAM040_5


title: 14-C01D02

description:
Library name: Sample 14
whole blood collected from timepoint C01D02


title: N2_5_CAM788_3

description: Library name: N2_5_CAM788_3


title: N2_2_CAM791_3

description: Library name: N2_2_CAM791_3


title: 12-C01D01

description:
Library name: Sample 8
whole blood collected from timepoint C01D01


title: N2_1_CAM040_1

description: Library name: N2_1_CAM040_1


title: N2_2_CAM795_4

description: Library name: N2_2_CAM795_4


title: 11-C01D02

description:
Library name: Sample 7
whole blood collected from timepoint C01D02


title: SKO_23A2

description: Library name: SKO_CBD_2


title: N2_1_CAM040_3

description: Library name: N2_1_CAM040_3


title: N2_5_CAM795_6

description: Library name: N2_5_CAM795_6


title: SKO_23A5

description: Library name: SKO_CBD_3


title: SKO_20A3

description: Library name: SKO_Veh_1


title: SKO_23C1

description: Library name: SKO_Veh_2


title: 1-EOT

description:
Library name: Sample 3
whole blood collected from timepoint EOT


title: SKO_20A1

description: Library name: SKO_CBD_1


title: 10-C01D02

description:
Library name: Sample 5
whole blood collected from timepoint C01D02


title: 10-C01D01

description:
Library name: Sample 4
whole blood collected from timepoint C01D01


title: 12-C01D02

description:
Library name: Sample 9
whole blood collected from timepoint C01D02


title: FMR_17A6

description: Library name: WT_Veh_3


title: 1-C01D01

description:
Library name: Sample 1
whole blood collected from timepoint C01D01


title: 1-C01D02

description:
Library name: Sample 2
whole blood collected from timepoint C01D02


title: FMR_17A4

description: Library name: WT_CBD_4


title: FMR_17A2

description: Library name: WT_CBD_3


title: NIB216 CORE cell line, treated (200V) rep3

city: Ljubljana

first: Anja

last: Blažič

address: Tržaška cesta 25

country: Slovenia

institute: University of Ljubljana, Faculty of electrical engineering

description: Library name: B12_EP

data_processing:
The libraries were then sequenced on an Illumina NovaSeq platform, generating 150 bp paired-end reads. Raw reads were processed using fastp for adapter trimming and quality filtering. Clean reads were aligned to the reference genome using HISAT2 (v2.0.5), and transcript assembly was performed with StringTie (v1.3.3b). Gene-level read counts were generated with featureCounts (v1.5.0-p3), and gene expression was quantified as fragments per kilobase of transcript per million mapped reads (FPKM), which accounts for both transcript length and sequencing depth.
Differential gene expression analysis was performed in NovoMagic (https://eu-magic.novogene.com/) using DESeq2 (v1.20.0), based on a negative binomial model.
Assembly: HISAT2 (v2.0.5)
Supplementary files format and content: Gene expression matrix_All samples.xlsx                                                                                Description: This file contains the raw gene expression matrix for all glioblastoma samples included in the study. The values represent raw read counts obtained from RNA sequencing, before any normalization. Rows: Each row corresponds to one gene, identified by its Ensembl Gene ID (column: gene_id). Columns: Sample-wise raw expression values are given in columns labeled by sample names (e.g. A1_C_R1, A2_EP_R1, etc.). Additional columns provide gene annotations including gene name, chromosome (gene_chr), start and end positions (gene_start, gene_end), strand, gene biotype, and gene description. Notes: Raw counts were obtained from aligned reads using a standard quantification tool (e.g., featureCounts). These values were used as the basis for normalization and differential expression analysis.
Supplementary files format and content: FPKMs_All samples.xlsx                                                                                Description: This file contains normalized expression values and differential expression results for patient-derived glioblastoma samples. It includes two sheets: NIB216 CORE and NIB140 CORE, representing two independent glioblastoma cultures. Rows: Each row corresponds to one gene, identified by its Ensembl Gene ID (gene_id). Columns: The sheets include normalized expression values (FPKM), log2 fold change (log2FoldChange), p-values (pvalue), and adjusted p-values (padj) from DESeq2 differential expression analysis. For each sample, raw read counts are listed (e.g., A1_C_R1_count) as well as FPKM-normalized values (e.g., A1_C_R1_fpkm). Notes: Normalization and differential expression were performed using DESeq2. The data represents comparisons between control and electroporated samples in each GB culture. Gene annotation columns are included to facilitate interpretation.

source_name: NIB216 CORE

growth_protocol: Cells were routinely passaged every 3 to 4 days and were maintained in a humidified environment at 37 °C with 5 % CO₂.

extract_protocol:
Total RNA was extracted from GB cells using the E.Z.N.A.® Total RNA Kit I (Omega Bio-Tek, Norcross, GA, USA; Cat. No. R6834) 24 hours after the electroporation.
Transcriptome analysis was performed by NovoGene (Munich, Germany). Total RNA was extracted from electroporated and sham control samples and subjected to quality control using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and reverse transcribed into cDNA. After second-strand synthesis and adaptor ligation, libraries containing 370–420 bp fragments were purified using the AMPure XP system and subsequently amplified by PCR. Following amplification, PCR products were purified again. Library quality was assessed using the Agilent Bioanalyzer 2100, and clustering was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (CA, USA).

treatment_protocol: For experiments, glioblastoma cells were trypsinized, counted, and centrifuged at 300 × g for 3 minutes. The resulting pellet was resuspended in DMEM (Gibco, #41965039) supplemented with 10 % foetal bovine serum (Gibco, #10500064) and 10 mM HEPES (Sigma-Aldrich, #H0887) to achieve a final cell density of 1 × 10⁶ cells/ml. Cells were exposed to H-FIRE pulses - 100 bursts of biphasic pulses, with 2 µs negative and 2 µs positive phase, 5 µs inter-phase and 5 µs interpulse delay, 25 pulses/burst, at 1 Hz burst repetition frequency and amplitude of 200 V (1 kV/cm). Ten minutes following pulse exposure, 850 µL of DMEM140+ was added directly to the electroporation cuvette. The full volume was then transferred to a single well in 6-well plate, and an additional 2 mL of DMEM10 was added, bringing the total volume per well to 3 mL. Sham-treated control (0V) cells were handled identically but were not subjected to pulse exposure.

value: NIB216 CORE

value: glioblastoma

value: treated (200V)


title: NIB216 CORE cell line, non-treated (0V) rep3

description: Library name: B11_C

value: non-treated (0V)


title: NIB140 CORE cell line, treated (200V) rep3

description: Library name: A10_EP

source_name: NIB140 CORE

value: NIB140 CORE


title: NIB216 CORE cell line, treated (200V) rep2

description: Library name: B8_EP


title: SKO_24A1

description: Library name: SKO_Veh_3


title: AMT33_20151208

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 83
Column name in raw_counts_rnaseqc_melanoma.csv:  AMT33_20151208

data_processing:
RNA-SeQC v1.2
Supplementary files format and content: comma-separated text file includes TPM for each Sample

source_name: melanoma

extract_protocol:
Tissue was collected fresh in phosphate-buffered saline. Bulk RNA sequencing was performed on tissue preserved in FFPE blocks.
RNA libraries for RNA-seq were prepared using TotalRNAseq Library Prep Kit following manufacturer's protocols.

value: melanoma


title: NIB216 CORE cell line, non-treated (0V) rep2

description: Library name: B7_C


title: FMR_16D4

description: Library name: FMR_CBD_5


title: AMT33_20150407

description:
Library name: Sample 82
Column name in raw_counts_rnaseqc_melanoma.csv:  AMT33_20150407


title: AMNN1_20160915

description:
Library name: Sample 81
Column name in raw_counts_rnaseqc_melanoma.csv:  AMNN1_20160915


title: FMR_16D2

description: Library name: FMR_Veh_3


title: AMHHH1_20190527

description:
Library name: Sample 80
Column name in raw_counts_rnaseqc_melanoma.csv:  AMHHH1_20190527


title: NIB140 CORE cell line, treated (200V) rep2

description: Library name: A6_EP


title: NIB140 CORE cell line, non-treated (0V) rep2

description: Library name: A5_C


title: NIB216 CORE cell line, treated (200V) rep1

description: Library name: B4_EP


title: FMR_16A6

description: Library name: FMR_CBD_4


title: NIB216 CORE cell line, non-treated (0V) rep1

description: Library name: B3_C


title: AM946_20181024

description:
Library name: Sample 78
Column name in raw_counts_rnaseqc_melanoma.csv:  AM946_20181024


title: FMR_15E8

description: Library name: FMR_Veh_1


title: AM986_20190202

description:
Library name: Sample 79
Column name in raw_counts_rnaseqc_melanoma.csv:  AM986_20190202


title: FMR_15B3

description: Library name: FMR_CBD_3


title: AM880_20191101

description:
Library name: Sample 76
Column name in raw_counts_rnaseqc_melanoma.csv:  AM880_20191101


title: AM931_20190701

description:
Library name: Sample 77
Column name in raw_counts_rnaseqc_melanoma.csv:  AM931_20190701


title: FMR_15B1

description: Library name: FMR_CBD_2


title: NIB140 CORE cell line, non-treated (0V) rep1

description: Library name: A1_C


title: AM78_20131211

description:
Library name: Sample 75
Column name in raw_counts_rnaseqc_melanoma.csv:  AM78_20131211


title: NIB140 CORE cell line, treated (200V) rep1

description: Library name: A2_EP


title: NIB140 CORE cell line, non-treated (0V) rep3

description: Library name: A9_C


title: FMR_15A5

description: Library name: FMR_CBD_1


title: FMR_14F3

description: Library name: WT_Veh_2


title: AM760_20181007

description:
Library name: Sample 74
Column name in raw_counts_rnaseqc_melanoma.csv:  AM760_20181007


title: paclitaxel resistant A549 cells, experimental group, rep3

city: Jinan

first: Yue

last: Liu

state: Shandong

address: No. 44 West Wenhua Road

department: School of Pharmaceutical Science

institute: Shandong University

description:
Library name: TAX-3
paclitaxel resistant

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: cell line

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

value: human lung adenocarcinoma epithelial cells

value: paclitaxel resistant cells


title: FMR_14C1

description: Library name: WT_CBD_2

value: hippocampal tissue


title: paclitaxel resistant A549 cells, experimental group, rep2

description:
Library name: TAX-2
paclitaxel resistant


title: paclitaxel resistant A549 cells, experimental group, rep1

description:
Library name: TAX-1
paclitaxel resistant


title: AM760_20180531

description:
Library name: Sample 73
Column name in raw_counts_rnaseqc_melanoma.csv:  AM760_20180531


title: paclitaxel sensitive A549 cells, control group, rep3

description:
Library name: A549-3
paclitaxel sensitive control

value: paclitaxel sensitive cells


title: FMR_16A8

description: Library name: FMR_Veh_2

value: Veh


title: AM752_20171214

description:
Library name: Sample 72
Column name in raw_counts_rnaseqc_melanoma.csv:  AM752_20171214


title: FMR_14B3

description: Library name: WT_Veh_1


title: AM747_20180328

description:
Library name: Sample 71
Column name in raw_counts_rnaseqc_melanoma.csv:  AM747_20180328


title: paclitaxel sensitive A549 cells, control group, rep2

description:
Library name: A549-2
paclitaxel sensitive control


title: FMR_14A3

description: Library name: WT_CBD_6


title: paclitaxel sensitive A549 cells, control group, rep1

description:
Library name: A549-1
paclitaxel sensitive control


title: AM726_20180308

description:
Library name: Sample 69
Column name in raw_counts_rnaseqc_melanoma.csv:  AM726_20180308


title: FMR_13C6

description: Library name: WT_Veh_6


title: AM662_20171021

description:
Library name: Sample 68
Column name in raw_counts_rnaseqc_melanoma.csv:  AM662_20171021


title: AM727_20180213

description:
Library name: Sample 70
Column name in raw_counts_rnaseqc_melanoma.csv:  AM727_20180213


title: RPE1-SLC39A9-KO-1

city: Montreal

first: Rhalena

middle: Amber

last: Thomas

state: QC

address: 3801 rue University, Montreal Neurological Institute, NW B150

department: Neurology

institute: McGill University

description:
Library name: KOS1
colnumn name in RPKM counts S1

data_processing:
GenPipes rna seq pipeline - Stringtie version 4.0.0
Timmomatic trim and merge readsets; Star alignment to reference genome; Picard processing and QC metrics; Wiggle to make tracks
Raw counts in each feature calculated using HT Seq Count
combined raw counts matrix with standardize read counts pased on sturation plots from wiggle tracks
Assembly: GRCh37
Supplementary files format and content: Raw RNA read counts for each sample in csv file
Supplementary files format and content: matrix of combined raw counts tsv file format where is sample is a column

extract_protocol:
RNA extraction Qiagen kit
Illumina paired end high content

value: retinal epithelial cells

value: genemodification


title: FMR_13C5

description: Library name: WT_Veh_5


title: RPE1-SLC39A9-KO-3

description:
Library name: KOS3
colnumn name in RPKM counts S3


title: AM655_20171016

description:
Library name: Sample 66
Column name in raw_counts_rnaseqc_melanoma.csv:  AM655_20171016


title: AM655_20171127

description:
Library name: Sample 67
Column name in raw_counts_rnaseqc_melanoma.csv:  AM655_20171127


title: FMR_13C3

description: Library name: WT_Veh_4


title: RPE1-C3orf58-KO-3

description:
Library name: KOC3
colnumn name in RPKM counts C3


title: RPE1-C3orf58-KO-2

description:
Library name: KOC2
colnumn name in RPKM counts C2


title: RPE1-SLC39A9-KO-2

description:
Library name: KOS2
colnumn name in RPKM counts S2


title: FMR_12B7

description: Library name: FMR_Veh_6


title: FMR_12B4

description: Library name: FMR_CBD_6

value: CBD


title: RPE1-C3orf58-KO-1

description:
Library name: KOC1
colnumn name in RPKM counts C1


title: AM654_20170502

description:
Library name: Sample 64
Column name in raw_counts_rnaseqc_melanoma.csv:  AM654_20170502


title: RPE1-WT-3

description:
Library name: WT3
colnumn name in RPKM counts WT3

value: wildtype


title: FMR_12B1

description: Library name: FMR_Veh_4


title: FMR_13C2

description: Library name: WT_CBD_5

value: WT


title: AM654_20170607

description:
Library name: Sample 65
Column name in raw_counts_rnaseqc_melanoma.csv:  AM654_20170607


title: AM651N_20170629

description:
Library name: Sample 62
Column name in raw_counts_rnaseqc_melanoma.csv:  AM651N_20170629


title: FMR_12B3

description: Library name: FMR_Veh_5


title: CB_6A2

description: Library name: WT_CBD_1


title: AM642_20170530

description:
Library name: Sample 61
Column name in raw_counts_rnaseqc_melanoma.csv:  AM642_20170530


title: RPE1-WT-1

description:
Library name: WT1
colnumn name in RPKM counts WT1


title: AM651T_20170629

description:
Library name: Sample 63
Column name in raw_counts_rnaseqc_melanoma.csv:  AM651T_20170629


title: cortex, methylphenidate 3

city: Shinagawa-ku

first: Ryota

last: Nakano

state: Tokyo

address: Hatanodai 1-5-8

department: Showa University Graduate School of Pharmacy

country: Japan

institute: Showa university

description:
Library name: Sample 6
M3__count

data_processing:
Illumina bcl2fastq2-v2.19 software was used for basecalling.
Transcriptome sequencing (150 bp paired-end sequencing) was performed on a NovaSeq 6000 (Illumina Inc.).
Adapter sequences and low-quality bases in paired-end reads were removed with fastp (version 0.23.4).
Filtered paired-end reads were mapped to the mouse reference genome (GRCm39) by HISAT2 (version 2.2.1) and expression levels were quantified by StringTie (version 2.2.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Counts values for each Sample

source_name: cerebral cortex

growth_protocol: Mice were housed in plastic cages in a temperature-controlled room (22±1 ℃) and maintained at a 12-h light-dark cycle, with free access to food and water.

extract_protocol:
Cerebral cortex collected from 6-week-old F2 mice was flash-frozen in liquid nitrogen and stored at -80℃ until total RNA was extracted. Total RNA was isolated from the tissue using RNeasy Mini Kit (QIAGEN Inc., CA USA)"
Poly(A) RNA was prepared by the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). Sequencing libraries were prepared by the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: Six-week-old male ICR mice (F0) were administered MPH (15 mg/kg) or saline (10 mL/kg) subcutaneously for 21 consecutive days. After treatment, the male mice were mated with drug-untreated female mice, and offspring (F1) were obtained. One male mouse was randomly selected from each mother's litter and mated with a drug-untreated female mouse to obtain grand offspring (F2). At 6 weeks old, brain samples of F2 mice were collected for RNA-seq.

value: cerebral cortex

value: wild type

value: methylphenidate (15 mg/kg)

value: ICR

value: female


title: cortex, methylphenidate 2

description:
Library name: Sample 5
M2__count


title: RPE1-WT-2

description:
Library name: WT2
colnumn name in RPKM counts WT2


title: AM601_20170530

description:
Library name: Sample 60
Column name in raw_counts_rnaseqc_melanoma.csv:  AM601_20170530

value: melanoma


title: s038

description:
Library name: Sample 38
PBMCs collected from timepoint C01D08

data_processing:
Data processing involved uploading FASTQ files to the 10X Genomics cloud platform using Cell Ranger, without applying depth normalization, for the generation of the gene by cell matrix. The count matrix was then processed through the Seurat package in R for subsequent analysis.
Assembly: Ensembl - Grch38
Supplementary files format and content: Processed and normalized gene by cell matrix, along witg meta data is provided as a "Seurat" object - "Talla_etal_Singlecell_Seurat.RDS"

source_name: PBMCs

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using standard density gradient centrifugation. Following isolation, cells were filtered according to the 10x Genomics sample preparation protocol to remove debris and aggregates. Only highly viable cells were selected for downstream single-cell RNA sequencing.
The sequencing protocol adhered to the recommended guidelines of the 3’ V3 chemistry kit by 10X Genomics. Initially, single-cell Gel Beads-in-Emulsion (GEMs) were generated by combining 350K – 400K PBMCs, barcoded Single Cell 3’ v3.1 beads, and partitioning oil. These GEMs underwent processing via a 10X Chromium Controller machine (10X Genomics). Subsequent steps encompassed gel bead elimination, cell lysis, and reverse transcription in a C1000 Touch Thermal Cycler (BioRad) to yield barcoded cDNA. To extract oil residues, the GEM mixture underwent purification using Dynabeads, followed by cDNA amplification. Post-amplification cDNA was purified using the SPRIselect reagent. Evaluation of cDNA quality and quantity occurred via a 2100 Bioanalyzer Instrument (Agilent Technologies). Further stages entailed fragmentation, end repair, A-tailing, and adaptor ligation in accordance with the manufacturer's protocol. Library quality was verified using the Bioanalyzer. Final libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end reads to achieve high-throughput transcriptomic profiling at single-cell resolution.

value: PBMCs

value: HIV infected


title: AM592_20191112

description:
Library name: Sample 59
Column name in raw_counts_rnaseqc_melanoma.csv:  AM592_20191112


title: cortex, methylphenidate 1

description:
Library name: Sample 4
M1__count


title: s037

description:
Library name: Sample 37
PBMCs collected from timepoint C01D08


title: s036

description:
Library name: Sample 36
PBMCs collected from timepoint C01D08


title: AM592_20191021

description:
Library name: Sample 58
Column name in raw_counts_rnaseqc_melanoma.csv:  AM592_20191021


title: cortex, control 3

description:
Library name: Sample 3
C3__count

value: saline (10 ml/kg)


title: AM584_20170706

description:
Library name: Sample 56
Column name in raw_counts_rnaseqc_melanoma.csv:  AM584_20170706


title: s035

description:
Library name: Sample 35
PBMCs collected from timepoint C01D08


title: AM590_20190702

description:
Library name: Sample 57
Column name in raw_counts_rnaseqc_melanoma.csv:  AM590_20190702


title: s034

description:
Library name: Sample 34
PBMCs collected from timepoint C01D08


title: cortex, control 2

description:
Library name: Sample 2
C2__count


title: cortex, control 1

description:
Library name: Sample 1
C1__count


title: s033

description:
Library name: Sample 33
PBMCs collected from timepoint C01D08


title: Uterus, Doxorubicin and AMH, 4 hour

city: Boston

first: Ngoc Minh Phuong

last: Nguyen

address: 55 Fruit st

department: Pediatric Surgical Research Laboratory

institute: Massachusetts General Hospital andHarvard Medical School

description:
Library name: Uterus_DOX_MIS_4hr
10X Genomics

data_processing:
Data analysis was performed using CellRanger (version 7.0.0) with standard parameters by the Bauer Core Facility at Harvard University.
Assembly: mm10-2020-A
Supplementary files format and content: tab-separated values files and matrix files

source_name: Uterus

extract_protocol:
One uterus per animal was pooled for each group (N = 5 per group), were cut into small pieces and placed in 2 mL of DMEM (10% FBS, 1% penicillin/streptomycin), supplemented with 21 U/mL of Papain (Worthington, LK003178) and 1 mg/mL of collagenase A (Sigma Aldrich, 10103578001), and incubated for 30 minutes at 37°C. The samples were then mechanically dissociated using the gentleMACS™ Dissociator (Miltenyi Biotec). The cell suspension was filtered, and 10,000 cells from each group were collected for next steps of scRNASeq.
Samples were processed for scRNAseq according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10×Genomics) and Chromium Controller (10× Genomics). Single-cell libraries were sequenced using the NovaSeq S4 (Illumina) by the Bauer Core Facility at Harvard University.

value: Uterus

value: Doxorubicin (3mg/kg) and AMH (0.75mg/kg)


title: AM572_20161118

description:
Library name: Sample 53
Column name in raw_counts_rnaseqc_melanoma.csv:  AM572_20161118


title: AM584_20170301

description:
Library name: Sample 55
Column name in raw_counts_rnaseqc_melanoma.csv:  AM584_20170301


title: Uterus (Treated with AMH), biol rep 5, 24 hour

description: Library name: M5_24h_UT

data_processing:
Data processing was performed by Novogene Corporation Inc.
Assembly: mm10
Supplementary files format and content: a single CSV file contains the FPKM values for all samples

extract_protocol:
RNA was extracted using the Qiagen RNA extraction kit according to the manufacturer’s instructions
Library construction was performed by Novogene Corporation Inc.

value: AMH (0.75mg/kg)

value: 24 hour


title: AM57_20161019

description:
Library name: Sample 54
Column name in raw_counts_rnaseqc_melanoma.csv:  AM57_20161019


title: AM565_20190723

description:
Library name: Sample 52
Column name in raw_counts_rnaseqc_melanoma.csv:  AM565_20190723


title: s029

description:
Library name: Sample 29
PBMCs collected from timepoint C01D08


title: s031

description:
Library name: Sample 31
PBMCs collected from timepoint C01D08


title: Uterus (Treated with AMH), biol rep 4, 24 hour

description: Library name: M4_24h_UT


title: s030

description:
Library name: Sample 30
PBMCs collected from timepoint C01D08


title: Uterus, Doxorubixin, 4 hour

description:
Library name: Uterus_DOX_4hr
10X Genomics

value: Doxorubicin (3mg/kg)


title: AM539_20180829

description:
Library name: Sample 51
Column name in raw_counts_rnaseqc_melanoma.csv:  AM539_20180829


title: Uterus (Treated with AMH), biol rep 3, 24 hour

description: Library name: M3_24h_UT


title: s028

description:
Library name: Sample 28
PBMCs collected from timepoint C01D08


title: AM523_20160812

description:
Library name: Sample 50
Column name in raw_counts_rnaseqc_melanoma.csv:  AM523_20160812


title: Uterus (Treated with AMH), biol rep 2, 24 hour

description: Library name: M2_24h_UT


title: s027

description:
Library name: Sample 27
PBMCs collected from timepoint C01D08


title: Uterus (Treated with AMH), biol rep 1, 24 hour

description: Library name: M1_24h_UT


title: AM507_20160701

description:
Library name: Sample 49
Column name in raw_counts_rnaseqc_melanoma.csv:  AM507_20160701


title: s026

description:
Library name: Sample 26
PBMCs collected from timepoint C01D08


title: AM495_20160504

description:
Library name: Sample 48
Column name in raw_counts_rnaseqc_melanoma.csv:  AM495_20160504


title: s025

description:
Library name: Sample 25
PBMCs collected from timepoint C01D02


title: AM492_20170504

description:
Library name: Sample 47
Column name in raw_counts_rnaseqc_melanoma.csv:  AM492_20170504


title: AM490_20160812

description:
Library name: Sample 46
Column name in raw_counts_rnaseqc_melanoma.csv:  AM490_20160812


title: s032

description:
Library name: Sample 32
PBMCs collected from timepoint C01D08


title: s024

description:
Library name: Sample 24
PBMCs collected from timepoint C01D02


title: Uterus (Treated with Doxorubicin and AMH), biol rep 4, 24 hour

description: Library name: DM4_24h_UT

value: Doxorubicin ((3mg/kg) and AMH (0.75mg/kg)


title: Uterus (Treated with Doxorubicin and AMH), biol rep 3, 24 hour

description: Library name: DM3_24h_UT


title: s023

description:
Library name: Sample 23
PBMCs collected from timepoint C01D02


title: AM470_20171222

description:
Library name: Sample 45
Column name in raw_counts_rnaseqc_melanoma.csv:  AM470_20171222


title: Uterus (Treated with Doxorubicin and AMH), biol rep 2, 24 hour

description: Library name: DM2_24h_UT


title: Uterus (Treated with Doxorubicin and AMH), biol rep 1, 24 hour

description: Library name: DM1_24h_UT


title: s020

description:
Library name: Sample 20
PBMCs collected from timepoint C01D02


title: s022

description:
Library name: Sample 22
PBMCs collected from timepoint C01D02


title: s021

description:
Library name: Sample 21
PBMCs collected from timepoint C01D02


title: Uterus (Treated with Doxorubicin), biol rep 5, 24 hour

description: Library name: D5_24h_UT


title: AM463_20151231

description:
Library name: Sample 44
Column name in raw_counts_rnaseqc_melanoma.csv:  AM463_20151231


title: AM452_20171011

description:
Library name: Sample 43
Column name in raw_counts_rnaseqc_melanoma.csv:  AM452_20171011


title: s019

description:
Library name: Sample 19
PBMCs collected from timepoint C01D02


title: Uterus (Treated with Doxorubicin), biol rep 4, 24 hour

description: Library name: D4_24h_UT


title: Uterus (Treated with Doxorubicin), biol rep 3, 24 hour

description: Library name: D3_24h_UT


title: AM441_20151103

description:
Library name: Sample 42
Column name in raw_counts_rnaseqc_melanoma.csv:  AM441_20151103


title: s018

description:
Library name: Sample 18
PBMCs collected from timepoint C01D02


title: AM440_20160822

description:
Library name: Sample 41
Column name in raw_counts_rnaseqc_melanoma.csv:  AM440_20160822


title: Uterus (Treated with Doxorubicin), biol rep 2, 24 hour

description: Library name: D2_24h_UT


title: s017

description:
Library name: Sample 17
PBMCs collected from timepoint C01D02


title: AM430_20151019

description:
Library name: Sample 40
Column name in raw_counts_rnaseqc_melanoma.csv:  AM430_20151019


title: Uterus (Treated with Doxorubicin and AMH), biol rep 5, 24 hour

description: Library name: DM5_24h_UT


title: Uterus (Treated with Doxorubicin), biol rep 1, 24 hour

description: Library name: D1_24h_UT


title: s016

description:
Library name: Sample 16
PBMCs collected from timepoint C01D01

value: pre-treatment/baseline


title: Uterus (Control), biol rep 5, 24 hour

description: Library name: C5_24h_UT

value: Controls (PBS/Saline)


title: AM409_20151130

description:
Library name: Sample 37
Column name in raw_counts_rnaseqc_melanoma.csv:  AM409_20151130


title: AM422_20150928

description:
Library name: Sample 39
Column name in raw_counts_rnaseqc_melanoma.csv:  AM422_20150928


title: s015

description:
Library name: Sample 15
PBMCs collected from timepoint C01D01


title: Uterus (Control), biol rep 4, 24 hour

description: Library name: C4_24h_UT


title: s014

description:
Library name: Sample 14
PBMCs collected from timepoint C01D01


title: AM415_20170918

description:
Library name: Sample 38
Column name in raw_counts_rnaseqc_melanoma.csv:  AM415_20170918


title: AM409_20150908

description:
Library name: Sample 36
Column name in raw_counts_rnaseqc_melanoma.csv:  AM409_20150908


title: Uterus (Control), biol rep 3, 24 hour

description: Library name: C3_24h_UT


title: AM407_20150831

description:
Library name: Sample 35
Column name in raw_counts_rnaseqc_melanoma.csv:  AM407_20150831


title: s012

description:
Library name: Sample 12
PBMCs collected from timepoint C01D01


title: Uterus (Control), biol rep 1, 24 hour

description: Library name: C1_24h_UT


title: Uterus (Control), biol rep 2, 24 hour

description: Library name: C2_24h_UT


title: s011

description:
Library name: Sample 11
PBMCs collected from timepoint C01D01


title: 11-C01D01

description:
Library name: Sample 6
whole blood collected from timepoint C01D01

value: whole blood


title: s010

description:
Library name: Sample 10
PBMCs collected from timepoint C01D01


title: AM391_20151110

description:
Library name: Sample 34
Column name in raw_counts_rnaseqc_melanoma.csv:  AM391_20151110


title: AM38_20130329

description:
Library name: Sample 33
Column name in raw_counts_rnaseqc_melanoma.csv:  AM38_20130329


title: Uterus (Treated with AMH), biol rep 4, 4 hour

description: Library name: M4_4h_UT

value: 4 hour


title: s013

description:
Library name: Sample 13
PBMCs collected from timepoint C01D01


title: AM363_20150625

description:
Library name: Sample 32
Column name in raw_counts_rnaseqc_melanoma.csv:  AM363_20150625


title: AM346_20150605

description:
Library name: Sample 31
Column name in raw_counts_rnaseqc_melanoma.csv:  AM346_20150605


title: s009

description:
Library name: Sample 9
PBMCs collected from timepoint C01D01


title: Uterus (Treated with AMH), biol rep 3, 4 hour

description: Library name: M3_4h_UT


title: Uterus (Treated with AMH), biol rep 2, 4 hour

description: Library name: M2_4h_UT


title: s008

description:
Library name: Sample 8
PBMCs collected from timepoint C01D01


title: AM333_20180604

description:
Library name: Sample 30
Column name in raw_counts_rnaseqc_melanoma.csv:  AM333_20180604


title: s007

description:
Library name: Sample 7
PBMCs collected from timepoint C01D01


title: Uterus (Treated with AMH), biol rep 1, 4 hour

description: Library name: M1_4h_UT


title: AM333_20150514

description:
Library name: Sample 29
Column name in raw_counts_rnaseqc_melanoma.csv:  AM333_20150514


title: AM324_20150423

description:
Library name: Sample 28
Column name in raw_counts_rnaseqc_melanoma.csv:  AM324_20150423


title: s006

description:
Library name: Sample 6
PBMCs collected from timepoint C01D01


title: Uterus (Treated with Doxorubicin and AMH), biol rep 5, 4 hour

description: Library name: DM5_4h_UT


title: Uterus (Treated with Doxorubicin and AMH), biol rep 4, 4 hour

description: Library name: DM4_4h_UT


title: s005

description:
Library name: Sample 5
PBMCs collected from timepoint C01D01


title: s004

description:
Library name: Sample 4
PBMCs collected from timepoint C01D01


title: Uterus (Treated with AMH), biol rep 5, 4 hour

description: Library name: M5_4h_UT


title: AM301_20170427

description:
Library name: Sample 26
Column name in raw_counts_rnaseqc_melanoma.csv:  AM301_20170427


title: AM307_20170629

description:
Library name: Sample 27
Column name in raw_counts_rnaseqc_melanoma.csv:  AM307_20170629


title: AM291_20150218

description:
Library name: Sample 25
Column name in raw_counts_rnaseqc_melanoma.csv:  AM291_20150218


title: Uterus (Treated with Doxorubicin and AMH), biol rep 2, 4 hour

description: Library name: DM2_4h_UT


title: Uterus (Treated with Doxorubicin and AMH), biol rep 3, 4 hour

description: Library name: DM3_4h_UT


title: s003

description:
Library name: Sample 3
PBMCs collected from timepoint C01D01


title: AM282_20170127

description:
Library name: Sample 24
Column name in raw_counts_rnaseqc_melanoma.csv:  AM282_20170127


title: s002

description:
Library name: Sample 2
PBMCs collected from timepoint C01D01


title: AM253_20141217

description:
Library name: Sample 22
Column name in raw_counts_rnaseqc_melanoma.csv:  AM253_20141217


title: AM253_20160421

description:
Library name: Sample 23
Column name in raw_counts_rnaseqc_melanoma.csv:  AM253_20160421


title: Uterus (Treated with Doxorubicin), biol rep 5, 4 hour

description: Library name: D5_4h_UT


title: Uterus (Treated with Doxorubicin), biol rep 4, 4 hour

description: Library name: D4_4h_UT


title: Uterus (Treated with Doxorubicin and AMH), biol rep 1, 4 hour

description: Library name: DM1_4h_UT


title: thymus sample of donor35

city: Chengdu

first: Yujun

last: Deng

address: No. 17, Section 3, Renmin South Road, Chengdu

institute: Sichuan University

description:
Library name: donor35
10x Genomics
CITEseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 or v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: transcript files :Tab-separated values files and matrix files; TCR files :comma-separated values files
Library strategy: CITE-seq

source_name: thymus

extract_protocol:
Human thymus samples were collected and transferred to RPMI1640 medium supplied with 10% FBS on ice, the tissues were cut into small pieces to release thymocytes. After thymocytes were collected, the remaining tissues were washed with RPMI1640 for 2-3 times and subjected to digestion with pre-warmed RPMI1640 containing 0.1g/mL collagenase and 100ug/mL DNase at 37ºC for 30-40 mins. The cell suspension was passed through 70m cell strainer and combined with thymocytes collected previously. The cells were centrifuged at 500g for 6min and suspended with RPMI1640 medium for cell counting, staining and sorting.  PBMCs were isolated from peripheral blood using Lymphocyte Separation Medium (LTS1077, TBD). Briefly, blood was added into 15mL tube containing equal volume of Lymphocyte Separation Medium gently and centrifuged at 2000 rpm for 20 min at room temperature with brake off. The PBMCs layer located at the interface were collected and washed with PBS plus 5% FBS.  For scRNA-seq, fresh cells isolated from human thymus were sorted as 7-AAD-CD235a-CD45+ and 7-AAD-CD235a-CD45- cells and combined with ratio at 6:4, or sorted as CD34+ cells or EpCAM+ cells. The sorted cells were applied for 10X single cell RNA-sequencing, TCR repertoire sequencing or cellular indexing of transcriptomes and epitopes sequencing.
For 10X single cell RNA-sequencing and 5’-TCR repertoire sequencing, 20,000 live sorted thymic cells or PBMCs were loaded on to each of the Chromium Controller (10X Genomics). Single cell cDNA and unique molecular identifier (UMI) tagged scRNA-Seq libraries and TCR repertoire Seq libraries were prepared using 10X Genomics platform.

value: thymus

value: 3 years

value: Female


title: thymus sample of donor36

description:
Library name: donor36
10x Genomics
CITEseq

value: 2 months


title: Uterus (Treated with Doxorubicin), biol rep 2, 4 hour

description: Library name: D2_4h_UT


title: AM212_20171106

description:
Library name: Sample 21
Column name in raw_counts_rnaseqc_melanoma.csv:  AM212_20171106

value: melanoma


title: Uterus (Treated with Doxorubicin), biol rep 3, 4 hour

description: Library name: D3_4h_UT


title: thymus sample of donor34

description:
Library name: donor34
10x Genomics
CITEseq

value: 12 days

value: Male


title: AM212_20170817

description:
Library name: Sample 20
Column name in raw_counts_rnaseqc_melanoma.csv:  AM212_20170817


title: AM212_20160325

description:
Library name: Sample 19
Column name in raw_counts_rnaseqc_melanoma.csv:  AM212_20160325


title: Uterus (Treated with Doxorubicin), biol rep 1, 4 hour

description: Library name: D1_4h_UT

value: Uterus


title: AM204_20140905

description:
Library name: Sample 18
Column name in raw_counts_rnaseqc_melanoma.csv:  AM204_20140905


title: Uterus (Control), biol rep 5, 4 hour

description: Library name: C5_4h_UT


title: AM200_20140903

description:
Library name: Sample 17
Column name in raw_counts_rnaseqc_melanoma.csv:  AM200_20140903


title: Uterus (Control), biol rep 4, 4 hour

description: Library name: C4_4h_UT


title: thymus sample of donor31

description:
Library name: donor31
10x Genomics
CITEseq


title: peripheral blood sample of donor30

description:
Library name: donor30
10x Genomics
5'scRNA + scTCRseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 or v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: transcript files :Tab-separated values files and matrix files; TCR files :comma-separated values files

source_name: peripheral blood

value: peripheral blood

value: PBMC

value: 1 years


title: Uterus (Control), biol rep 2, 4 hour

description: Library name: C2_4h_UT


title: AM194_20160815

description:
Library name: Sample 15
Column name in raw_counts_rnaseqc_melanoma.csv:  AM194_20160815


title: Uterus (Control), biol rep 1, 4 hour

description: Library name: C1_4h_UT


title: AM194_20160408

description:
Library name: Sample 14
Column name in raw_counts_rnaseqc_melanoma.csv:  AM194_20160408


title: peripheral blood sample of donor28

description:
Library name: donor28
10x Genomics
5'scRNA + scTCRseq

value: 10 months


title: peripheral blood sample of donor27

description:
Library name: donor27
10x Genomics
5'scRNA + scTCRseq

value: 5 years


title: AM176_20141114

description:
Library name: Sample 13
Column name in raw_counts_rnaseqc_melanoma.csv:  AM176_20141114


title: s001

description:
Library name: Sample 1
PBMCs collected from timepoint C01D01

value: PBMCs

value: HIV infected

value: pre-treatment/baseline


title: peripheral blood sample of donor29

description:
Library name: donor29
10x Genomics
5'scRNA + scTCRseq

value: 4 years


title: WT, Model, scRNAseq

city: Beijing

first: Xiaoyue

address: Shuaifuyuan NO.1, Dongcheng district

institute: Paking Union Medical College Hospital

data_processing:
Cell Ranger (v6.0.1) was used to process raw sequencing data and generate the count matrix. Next, data were normalized and scaled by NormalizeData and ScaleData function, then integrated into an un-banched matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: lung

extract_protocol:
Lung tissue from WT_Model and KO_Model mice (n=1, respectively) were harvested. Cell preparation followed by 10x Genomics® Cell Preparation Guide. The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ reagent kit (10X Genomics) according to the manufacturer’s instructions.
Sequencing was performed with Illumina (NovaSeq), according to the manufacturer’s instructions (Illumina). scRNA-seq library was constructed according to the instruction of the Single Cell 3’ Reagent Kit v3.1 (10x Genomics).

value: lung

value: wildtype

value: 22-24 weeks

value: female

tag: disease

value: SLE-PAH


title: peripheral blood sample of donor26

description:
Library name: donor26
10x Genomics
5'scRNA + scTCRseq


title: peripheral blood sample of donor24

description:
Library name: donor24
10x Genomics
5'scRNA + scTCRseq

value: 103 years

value: Female


title: AM166_20161007

description:
Library name: Sample 12
Column name in raw_counts_rnaseqc_melanoma.csv:  AM1586_20210203

value: melanoma


title: thymus sample of donor32

description:
Library name: donor32
10x Genomics
CITEseq

value: thymus

value: 1 month

value: Male


title: AM156_20150513

description:
Library name: Sample 10
Column name in raw_counts_rnaseqc_melanoma.csv:  AM156_20150513


title: AM1586_20210203

description:
Library name: Sample 11
Column name in raw_counts_rnaseqc_melanoma.csv:  AM1586_20210203


title: 18M_E1F2_2

city: changchun

first: Shuai

last: Zhang

state: jilin

address: No. 1035 Boshuo Road

department: Northeast Asian Institute of Traditional Chinese Medicine

institute: Changchun University of Chinese Medicine

description: Parallel sample 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools software were used to map to reference genome.
Gene function was annotated based on the following databases: NR (NCBI non-redundant protein sequences database); Nt (NCBI non-redundant nucleotide sequences); Pfam (The database of Homologous protein family); COG (The database of Clusters of Protein homology); Swiss-Prot (A manually annotated non-redundant protein sequence database); KOG (The database of Clusters of protein homology); KEGG (The database of Kyoto Encyclopedia of Genes and Genomes); GO (Gene Ontology database).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM for each sample

source_name: brain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
The first strand of cDNA was synthesised in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primers, and the second strand of cDNA was synthesised using dNTPs as raw material. The double-stranded cDNA was purified and subjected to PCR amplification to finally obtain the library. Qubit2.0 Fluorometer was used for preliminary quantification, and the library was diluted to 1.5 ng/ul. Agilent2100 bioanalyzer was used to insertsize the library to ensure the quality of the library.

value: brain

value: 200 mg/kg GRP-E1F2


title: peripheral blood sample of donor25

description:
Library name: donor25
10x Genomics
5'scRNA + scTCRseq

value: peripheral blood

value: PBMC

value: 102 years


title: peripheral blood sample of donor22

description:
Library name: donor22
10x Genomics
5'scRNA + scTCRseq

value: 104 years


title: thymus sample of donor33

description:
Library name: donor33
10x Genomics
CITEseq

value: 3 years


title: 18M_E1F2_3

description: Parallel sample 3


title: Uterus (Control), biol rep 3, 4 hour

description: Library name: C3_4h_UT

value: Uterus

value: Controls (PBS/Saline)

value: 4 hour


title: AM156_20140616

description:
Library name: Sample 8
Column name in raw_counts_rnaseqc_melanoma.csv:  AM156_20140616


title: 18M_E1F2_1

description: Parallel sample 1


title: AM196_20150121

description:
Library name: Sample 16
Column name in raw_counts_rnaseqc_melanoma.csv:  AM196_20150121


title: AM156_20141006

description:
Library name: Sample 9
Column name in raw_counts_rnaseqc_melanoma.csv:  AM156_20141006


title: KO, Model, scRNAseq

value: lung

value: TRAF5 knockout

value: 22-24 weeks

value: female

value: SLE-PAH


title: peripheral blood sample of donor23

description:
Library name: donor23
10x Genomics
5'scRNA + scTCRseq

value: 100 years

value: Female


title: AM137_20140507

description:
Library name: Sample 6
Column name in raw_counts_rnaseqc_melanoma.csv:  AM137_20140507

value: melanoma


title: 18M_Ctrl_2

description: Parallel sample 2

value: brain

value: physiological saline


title: 18M_Ctrl_1

description: Parallel sample 1


title: peripheral blood sample of donor19

description:
Library name: donor19
10x Genomics
5'scRNA + scTCRseq

value: peripheral blood

value: PBMC

value: 105 years


title: peripheral blood sample of donor20

description:
Library name: donor20
10x Genomics
5'scRNA + scTCRseq


title: AM131_20140716

description:
Library name: Sample 5
Column name in raw_counts_rnaseqc_melanoma.csv:  AM131_20140716


title: 5M_Ctrl_3

description: Parallel sample 3


title: 18M_Ctrl_3

description: Parallel sample 3


title: 5M_Ctrl_2

description: Parallel sample 2


title: thymus sample of donor18

description:
Library name: donor18
10x Genomics
5'scRNA + scTCRseq

value: thymus

value: combined CD45+ and CD45- cells (6:4)

value: 64 years


title: AM115_20140318

description:
Library name: Sample 4
Column name in raw_counts_rnaseqc_melanoma.csv:  AM115_20140318


title: peripheral blood sample of donor21

description:
Library name: donor21
10x Genomics
5'scRNA + scTCRseq

value: Male


title: AM1130_20190710

description:
Library name: Sample 3
Column name in raw_counts_rnaseqc_melanoma.csv:  AM1130_20190710


title: AM143_20140603

description:
Library name: Sample 7
Column name in raw_counts_rnaseqc_melanoma.csv:  AM143_20140603


title: thymus sample of donor16

description:
Library name: donor16-2
10x Genomics
5'scRNA + scTCRseq

value: 46 years


title: BMDMs, IFNr2_Input

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost 3length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include count values for each Sample

source_name: BMDM

growth_protocol: BMDMs were maintained in DMEM supplementred with 10%fetal bovine serum (FBS) under conditions of 37℃ in an atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construstion of sequencing livraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactruer's protocols
MeRIP-Seq

treatment_protocol: IFNγ 40ng/ml

value: BMDM

value: WT

value: IFNγ


title: AM1038_20190517

description:
Library name: Sample 1
Column name in raw_counts_rnaseqc_melanoma.csv:  AM1038_20190517


title: BMDMs, IFNr2_IP


title: peripheral blood sample of donor16

description:
Library name: donor16-1
10x Genomics
5'scRNA + scTCRseq


title: BMDMs, IFNr1_IP


title: BMDMs, Ctr2_IP

value: control


title: BMDMs, IFNr1_Input


title: thymus sample of donor14

description:
Library name: donor14-2
10x Genomics
5'scRNA + scTCRseq

value: 69 years


title: Non-AD_control

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
ftp://miRbase.org/pub/miRbase/CURRENT
The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 21.0
Supplementary files format and content: excel table; Normalization of sequence counts in each sample (or data set) is achieved by dividing the counts by a library size parameter of the corresponding sample. The library size parameter is a median value of the ratio between the counts a specific sample and a pseudo-reference sample. A count number in the pseudo-reference sample is the count geometric mean across all samples.

source_name: Brain tissue

extract_protocol:
all RNA extracted with Trizol and purified with with Qiagen Rneasy Kit
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA).
miRNA-Seq (the single-end sequencing 50bp on an Illumina Hiseq 2500 at the LC Sciences)

tag: background

value: Human cortex

tag: gender

value: cortex

tag: timepoint

value: post mortem

value: wild-type


title: thymus sample of donor15

description:
Library name: donor15-2
10x Genomics
5'scRNA + scTCRseq

tag: tissue

value: 53 years


title: peripheral blood sample of donor15

description:
Library name: donor15-1
10x Genomics
5'scRNA + scTCRseq

value: peripheral blood

value: PBMC


title: AD


title: peripheral blood sample of donor14

description:
Library name: donor14-1
10x Genomics
5'scRNA + scTCRseq


title: BMDMs, Ctr1_IP


title: thymus sample of donor13

description:
Library name: donor13-2
10x Genomics
5'scRNA + scTCRseq

value: thymus

value: 4 years

value: Female


title: peripheral blood sample of donor13

description:
Library name: donor13-1
10x Genomics
5'scRNA + scTCRseq


title: thymus sample of donor12

description:
Library name: donor12-2
10x Genomics
5'scRNA + scTCRseq

value: combined CD45+ and CD45- cells (6:4)

value: 22 years

value: Male


title: 5M_Ctrl_1

description: Parallel sample 1

value: brain

value: physiological saline


title: thymus sample of donor17

description:
Library name: donor17
10x Genomics
5'scRNA + scTCRseq

value: 21 months


title: input_DMSO_expjuin2018_SUPT1

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

data_processing:
Raw reads quality control perfomed with Fastqc (version 0.11.5)
Reads alignment with BWA (0.7.16a) on hg38 human genome version
Bigwig files were generated using deeptools bamCompare and normalized by the correponding input using SES normalization
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input

source_name: T-cell

growth_protocol: SupT1 cells were routinely maintained in RPMI 1640 Medium (Lonza) supplemented with 10% (v/v) heat-inactivated fetal calf serum (Lonza), 1000 U.mL-1 penicillin/streptomycin (Lonza) and 20 mM Ultraglutamine (Lonza).

extract_protocol:
ChIP experiments were performed in SupT1 T-ALL cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq librairies were constructed using the Next Gen DNA Library Kit (Active Motif 53216 and 53264).

treatment_protocol: Notch signaling was inhibited by treating SupT1 T-ALL cells with the γ-secretase inhibitor (GSI) compound E at the final concentration of 1µM for two days.

value: T-cell lymphoma cell line

value: DMSO

tag: passages


title: RGCs from Tgfbr1flx/flx;Vglut2+/+ mice, Sample3

city: Changsha

first: Yuerong

last: Ren

address: Renmin Road No.139

institute: central south university

data_processing:
The libraries were sequenced on a llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads, which were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis was performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Q-value <0.05 and |log2FC| > 1 was set as the threshold for significantly differential expression genes (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. Based on the hypergeometric distribution, GO pathway enrichment analysis of DEGs was performed to screen the significantly enriched term using R (v 3.2.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retinal ganglion cell

extract_protocol:
The total RNA of each sample was extracted by RNeasy Micro Kit (QIAGEN). The purity and quantification of RNA were assessed with Nanodrop 2000 (Thermo Scientific). The integrity of RNA was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies). 1ng of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: retinal ganglion cell


title: AM1098_20190712

description:
Library name: Sample 2
Column name in raw_counts_rnaseqc_melanoma.csv:  AM1098_20190712

value: melanoma


title: thymus sample of donor11

description:
Library name: donor11-2
10x Genomics
5'scRNA + scTCRseq

value: 9 years


title: H3K27me3_DMSO_expjuin2018_SUPT1

tag: strain

tag: chip antibody

value: H3K27me3 (Active Motif 39155)


title: peripheral blood sample of donor12

description:
Library name: donor12-1
10x Genomics
5'scRNA + scTCRseq

value: peripheral blood


title: RING1_GSI_exp05_SUPT1

value: GSI

value: RING1 (Bethyl A300-552A)


title: RGCs from Tgfbr1flx/flx;Vglut2+/+ mice, Sample2

tag: genotype


title: peripheral blood sample of donor11

description:
Library name: donor11-1
10x Genomics
5'scRNA + scTCRseq

value: PBMC

tag: Sex


title: HEK293T_PML_KO

source_name: HEK293T cells

value: Human kidney

value: Female

value: cell line

value: 3 days in vitro

value: Knock out


title: thymus sample of donor10

description:
Library name: donor10-2
10x Genomics
5'scRNA + scTCRseq

value: thymus

value: combined CD45+ and CD45- cells (6:4)

tag: age

value: 35 years


title: BMDMs, Ctr2_Input

tag: cell type

value: BMDM

value: WT

value: control


title: H3K27me3_GSI_expjuin2018_SUPT1

value: T-cell lymphoma cell line


title: RGCs from Tgfbr1flx/flx;Vglut2Cre/+ mice, Sample2

value: retinal ganglion cell


title: HEK293T_WT

value: wild-type


title: RGCs from Tgfbr1flx/flx;Vglut2Cre/+ mice, Sample3


title: peripheral blood sample of donor10

description:
Library name: donor10-1
10x Genomics
5'scRNA + scTCRseq

value: peripheral blood


title: RING1_DMSO_exp05_SUPT1

value: DMSO

value: RING1 (Bethyl A300-552A)


title: input_GSI_expjuin2018_SUPT1

value: GSI


title: thymus sample of donor9

description:
Library name: donor9-2
10x Genomics
5'scRNA + scTCRseq

value: 24 years

value: Female


title: mesenteric adipose tissues 3 (CON3)

city: 济南市

first: xiaofen

last: lv

address: 107 Wenhua West Road

data_processing:
These libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: adipose tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: adipose tissue

value: no injury


title: BMDMs, Ctr1_Input


title: MI2beta_GSI_exp05_SUPT1

value: MI2beta (Bethyl A301-081A)


title: mesenteric adipose tissues 2 (CON2)


title: peripheral blood sample of donor9

description:
Library name: donor9-1
10x Genomics
5'scRNA + scTCRseq

value: PBMC


title: MI2beta_DMSO_exp05_SUPT1


title: mesenteric adipose tissues 1 (CON1)