title: Mayo 0549

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

department: Immunology

institute: Mayo Clinic Arizona

description: Library name: Mayo 0549

data_processing:
Libraries were sequenced on an Illumina NovaSeq X Plus using a 25B 300-cycle kit, generating paired-end 151-bp FASTQ files. Base calling and FASTQ generation were performed by the sequencing facility using the Illumina FASTQ generation workflow available for the NovaSeq X Plus platform. FASTQ quality control was performed using FastQC, and files showed Sanger / Illumina 1.9 quality encoding. FASTQ files were processed using the Parse Biosciences Trailmaker online platform for Evercode Whole Transcriptome single-cell RNA-seq libraries. Reads were aligned to the mouse mm39/GRCm39 reference genome/transcriptome, cell barcodes and UMIs were processed, and UMIs were collapsed to generate gene-by-cell UMI count matrices. The DGE_filtered gene-by-cell UMI count matrices generated by the Parse Biosciences Trailmaker pipeline. The filtered matrices contain cells identified by the Trailmaker pipeline based on its default cell-calling/barcode filtering procedure.
Assembly: Mouse mm39/GRCm39
Supplementary files format and content: Tab separated files and matrix files

source_name: Spleen

growth_protocol: B6.SJL mice received adoptive transfers of WT or CD4-Cre P2rx7^fl/fl^ P14 cells and were infected with LCMV Clone 13 or LCMV Armstrong for 7 or 30 days. Mice were maintained in a temperature-controlled animal facility with ad libitum access to food and water.

extract_protocol:
Spleens were mechanically dissociated and passed through a 70-µm cell strainer to obtain single-cell suspensions. Cells were then stained with fluorochrome-conjugated antibodies for cell sorting.
Parsebioscience Evercode WT v3 protocol was used following manufacturer instructions. We fixed the cells using the Evercode Cell Fixation v3 kit, then stored samples at -80oC. Numbers and viability were quantified. After this, cells were distributed into microplates for Round 1 barcoding. They were then pooled, mixed and redistributed for Round 2 and Round 3 to append unique combinations of barcodes. After barcoding rounds, cells were lysed and the uniquely tagged cDNA was purified and amplified for sequencing.

treatment_protocol: LCMV-Armstrong or LCMV-Clone 13 infection

value: Spleen

value: CD8+ T cells


title: Parental_siNELFA_REP1

status: Public on Jul 08 2026

type: SRA

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Library name: NELFA_REP1_PRO-seq

library_source: other

data_processing:
Illumina adapters were trimmed from the 3' ends of paired-end reads using Cutadapt, employing the parameters: '-a GNNNNNNTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -A TNNNNNNGATCGTCGGACTGTAGAACTCTGAACGTGT -O 10 --minimum-length 10 --pair-filter=any'.
Unique Molecular Identifiers (UMIs) located at the first 7 bases of both reads were extracted using UMI-tools ('umi_tools extract --quality-filter-mask=10 --quality-encoding="phred33" --extract-method=string --bc-pattern=NNNNNNN --bc-pattern2=NNNNNNN').
The processed reads were aligned to the hg38 reference genome using Bowtie2 in '--very-sensitive' mode with '--non-deterministic --no-discordant --no-unal' flags. Reads with low mapping quality (MAPQ < 10) were removed via SAMtools. PCR duplicates were then identified and collapsed based on UMIs using the command: 'umi-tools dedup --paired'.
To determine the precise location of active RNAPII, single-base resolution BigWig files were generated from the first base of Read 1 using the bamCoverage function (deepTools) with parameters '--samFlagInclude 64 --offset 1 1 --binSize 1'.  Forward and reverse strand BigWig files were generated separately using the '--filterRNAstrand' option.
Assembly: hg38
Supplementary files format and content: bigwig files for forward and reverse strands
Library strategy: PRO-Seq

molecule: other

organism: Homo sapiens

source_name: HEK293 FlpIn-TREx

extract_protocol:
Nuclei were extracted following the 'Cell Permeabilization for PRO-seq' protocol from Nascent Transcriptomics Core at Harvard Medical School (https://ntc.hms.harvard.edu/file_url/141).
Quick PRO-seq libraries were prepared from 1 million nuclei following the protocol described by Judd et al. (bioRxiv, 2020). Four biotin-11-NTPs were used in the run-on reaction.

tag: cell line

value: HEK293 FlpIn-TREx


title: ChIP CR3 H3K4me2 120

city: Yonago

first: Junichiro

last: Ohzeki

address: 86 Nishi-cho

department: Chromosome Engineering Research Center

country: Japan

institute: Tottori University

description:
Library name: PC count ChIP CR3 H3K4me2 120
Competitive PCR product derived from ChIP DNA

library_source: genomic

data_processing:
Fastq files were generated by Miseq base calling.
Sequencing reads were trimmed with cutadapt 4.0 using Python 3.9.13.
Trimmed reads were matched against the indexed list of the position code DNA using bowtie.
The number of reads for each the position code was obtained using samtools idxstats (1.11).
Assembly: The index list of the position code DNA (See also supplementary Inofrmation)
Supplementary files format and content: Tab-delimited text file includes raw counts for each the position code.

molecule: genomic DNA

source_name: Connective tissue

growth_protocol: Human HT1080 and derived cells were cultured in the DMEM Glutamax I (10569010, Gibco) supplemented with the 10% tet-system approved Fetal Bovine Serum (631101, TAKARA) at 37˚ C and 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at RT. After quenching and hypotonic treatment, then cells were sonicated using a picoruptor 2 apparatus (Diagenode).
A DNA pool of triplicate ChIP was prepared and 10 μl of the pool was used for competitive PCR to the construction of sequencing library.

tag: tissue

value: Connective tissue

tag: cell type

value: Fibrosarcoma

tag: genotype

value: carrying HAC 1-20

tag: treatment

value: 3 hr after colcemid release

tag: chip antibody


title: Mouse sperm, Untreated, 2.5ul Tn5, rep1

city: Atlanta

first: Katerina

last: Tsimaratou

state: GA

address: Whitehead Biomedical Research Building,615 Michael Street

department: Human Genetics

country: USA

institute: Emory Univeristy

description: Library name: Sperm_ATAC_Untreated_2.5ul_rep1

data_processing:
All libraries were sequenced on an Illumina NovaSeq X Plus platform using 150-bp paired-end sequencing. Adapter sequences were trimmed using Trim Galore. Paired-end reads were aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters except -X 2000. PCR duplicates were removed using Picard Tools. BAM files were filtered to retain properly paired reads with mapping quality ≥30 while excluding reads mapping to mitochondrial DNA (chrM), chromosome Y (chrY), unplaced contigs, and ENCODE mm10 blacklist regions. Read alignments were adjusted by offsetting reads mapped to the positive strand by +4 bp and reads mapped to the negative strand by −5 bp. Reads were separated into 50–115 bp and 180–247 bp fragment-size classes. Peaks were identified from the 50–115 bp fragments using MACS2 with the parameters --nomodel --nolambda. Genome-wide normalized bigWig tracks were generated from filtered BAM files using deepTools bamCoverage with RPKM normalization, a bin size of 10 bp, --ignoreForNormalization chrY chrM, and --minMappingQuality 30. Biological replicates were merged to generate the processed bigWig files deposited in GEO. Mono-nucleosomal occupancy profiles were generated using DANPOS2.
Assembly: mm10
Supplementary files format and content: bigWig (.bw) files containing genome-wide normalized ATAC-seq signal tracks generated from merged biological replicates. Signal tracks were generated separately for the 50–115 bp and 180–247 bp fragment-size classes from filtered, deduplicated alignments and normalized using deepTools bamCoverage with RPKM normalization (10-bp bins). The files are aligned to the mouse mm10 reference genome.

organism: Mus musculus

source_name: cauda epididymal sperm

extract_protocol:
After sperm counting, nuclei were isolated from 100,000 untreated or treated mouse sperm by centrifugation and lysis in buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl₂) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Lysis was terminated with lysis buffer containing 0.1% Tween-20, and nuclei were pelleted by centrifugation. Purified nuclei were resuspended in the transposase reaction mixture containing 0.05% digitonin and incubated at 37°C for 35 min with shaking (1,000 rpm). Following transposition, genomic DNA was purified using proteinase K digestion followed by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation
Libraries were PCR-amplified using the 2× KAPA SYBR FAST ABI Prism Kit (Kapa Biosystems) and 2.5 µM indexed primers under the following conditions: 72°C for 5 min, 98°C for 30 s, followed by 13 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Libraries were sequenced on an Illumina NovaSeq X Plus platform using 150-bp paired-end sequencing.

value: cauda epididymal sperm

value: Untreated, 2.5ul Tn5


title: 4Cseq_bulk_NHA_DMSO_HOTAIR_viewpoint

city: Boston

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: Sample 16

data_processing:
First 20 nucleotides were trimmed from Forward Read
Trimmed reads were aligned with Bowtie2 (defaults)
Resulting BAMs were processed with r3Cseq (Thongjuea et al., 2013)
Assembly: GRCh37 (hg19)
Supplementary files format and content: bedgraph.gz
Library strategy: 4C-Seq

source_name: NHA

growth_protocol: GBM8 were maintained as neurospheres in serum-free Neurobasal medium (Gibco) supplemented with: B-27 Plus and N-2 supplements (Gibco), 3 mM GlutaMAX (Gibco), 20 ng/mL recombinant human FGF2 and EGF (Sigma-Aldrich), 2 μg/mL heparin (Sigma-Aldrich), 50 units/mL penicillin/streptomycin (Gibco). Normal human astrocytes, immortalized via E6/E7 and hTERT expression (a generous gift from Dr. Yukihiko Sonoda), served as non-malignant controls. These cells were cultured in Astrocyte Medium (ScienCell, Cat# 1801) according to the manufacturer’s instructions.

extract_protocol:
described in Peter Krijger et al., 2020
described in Peter Krijger et al., 2020

treatment_protocol: GBM8 or NHA cells were treated with siRNAs for 48 hours. NHA cells were treated with All trans retinoic acid (SigmaAldrich,  R2500-25MG) diluted in DMSO according to manufacturer's protocol. GBM8 cells were incubated with Proteinase K (Thermo Scientific, EO0491) for 48 hours

value: NHA

value: immortalized human astrocytes

value: WT

value: DMSO


title: Mayo 0548

description: Library name: Mayo 0548

library_source: transcriptomic single cell

molecule: total RNA

tag: batch


title: Parental_siINTS12_REP2

description: Library name: INTS12_REP2_PRO-seq


title: ChIP CR3 CENPA 120

description:
Library name: PC count ChIP CR3 CENPA 120
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: 4Cseq_bulk_GBM8_ProteinaseK_LINC01116_viewpoint

description: Library name: Sample 15

value: low-passage glioma-initiating stem-like cells

value: Proteinase K


title: Mayo 0547

description: Library name: Mayo 0547


title: Parental_siINTS12_REP1

description: Library name: INTS12_REP1_PRO-seq


title: 4Cseq_bulk_GBM8_ProteinaseK_HOXDas2_viewpoint

description: Library name: Sample 14


title: ChIP COL H3K9me3 120

description:
Library name: PC count ChIP COL H3K9me3 120
Competitive PCR product derived from ChIP DNA

value: Colcemid


title: RNA-Seq, Parental_siCTRL_REP1

description:
Library name: CTRL_REP1
Nascent RNA

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR (Dobin et al., 2012)
RPKM normalised bigwig files generated using deepTools bamCoverage function with options: --normalizeUsing RPKM --exactScaling –effectiveGenomeSize (Ramirez et al., 2014)
Note: The first 11nt in the 5'-end of reads are the UMIs
Assembly: GRCh38
Supplementary files format and content: bigwig files for forward and reverse strands

extract_protocol:
As descriebd in Gregersen et al., 2020, Nat Protoc.
NEBNext Ultra II Direcional RNA Library Prep Kit for Illumina with UMI Adaptors

value: Parental


title: Mayo 0546

description: Library name: Mayo 0546

value: Spleen

value: CD8+ T cells


title: ChIP COL H3K36me2 120

description:
Library name: PC count ChIP COL H3K36me2 120
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: Parental_siCTRL_REP2

description: Library name: CTRL_REP2_PRO-seq

value: HEK293 FlpIn-TREx


title: 4Cseq_bulk_GBM8_ProteinaseK_HOXBas1_viewpoint

description: Library name: Sample 13


title: Mayo 0545

description: Library name: Mayo 0545


title: Parental_siCTRL_REP1

description: Library name: CTRL_REP1_PRO-seq


title: ChIP COL K4K20me1 120

description:
Library name: PC count ChIP COL K4K20me1 120
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma

value: carrying HAC 1-20


title: 4Cseq_bulk_GBM8_ProteinaseK_HOTAIRM1_viewpoint

description: Library name: Sample 12


title: Mayo 0544

description: Library name: Mayo 0544


title: ChIP COL H4K8ac 120

description:
Library name: PC count ChIP COL H4K8ac 120
Competitive PCR product derived from ChIP DNA


title: PRDM16 OE 3

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: Library name: Sample 12

library_source: transcriptomic

data_processing:
Illumina bcl2fastq (v2.20) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v4.4, v4.6) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5, v2.5.1), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v2.0.3, 2.0.5) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: Human iPS derived cardiomyocytes

extract_protocol:
miRNeasy micro kit (Qiagen)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: Human iPS derived cardiomyocytes


title: 4Cseq_bulk_GBM8_ProteinaseK_HOTAIR_viewpoint

description: Library name: Sample 11


title: Mayo 0543

description: Library name: Mayo 0543


title: PRDM16 OE 2

description: Library name: Sample 11


title: ChIP COL H3K14ac 120

description:
Library name: PC count ChIP COL H3K14ac 120
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: 4Cseq_bulk_GBM8_Pool_of_siRNAs_LINC01116_viewpoint

description: Library name: Sample 10

value: Pool of siRNAs


title: PRDM16 OE 1

description: Library name: Sample 10


title: Mayo 0410

description: Library name: Mayo 0410


title: ChIP COL H3K4me2 120

description:
Library name: PC count ChIP COL H3K4me2 120
Competitive PCR product derived from ChIP DNA


title: 4Cseq_bulk_GBM8_Pool_of_siRNAs_HOXDas2_viewpoint

description: Library name: Sample 9


title: control-GFP 3

description: Library name: Sample 9


title: Sample 8 KO

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Library name: Sample 8

data_processing:
snRNA-seq fastq files were precessed by using Cell Ranger (v9.0.0)
Ambient RNA or random barcode swapping counts were eliminated by using CellBender
Doublets were removed by using the R package scDblFinder.
Nornalization, PCA, cell clustering, and UMAP were perform with the R packege Seurat
Assembly: GRCm39
Supplementary files format and content: RDS file of Seurat object

molecule: nuclear RNA

source_name: Pancreatic Islets

extract_protocol:
Single nuclei were isolated from tissue samples using Miltenyi Nuclei extraction buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) and resuspended in PBS + 1% BSA containing 0.4U/uL of RNase Inhibitor (NEB). Quality and quantity of nuclei was assessed by Acridine Orange and propidium iodide dye on a Cellometer Auto 2000 (Nexcelom).
30,000 nuclei were loaded on a 10x Chromium Controller using 10X Genomics 3’ GEX v3.1 Platform (10x Genomics). Libraries were prepared by using 10x Chromium Next GEM Single Cell 3' GEM v4 kit.

value: Pancreatic Islets

value: KO


title: ChIP COL CENPA 120

description:
Library name: PC count ChIP COL CENPA 120
Competitive PCR product derived from ChIP DNA


title: 4Cseq_bulk_GBM8_Pool_of_siRNAs_HOXBas1_viewpoint

description: Library name: Sample 8

value: WT


title: Sample 2 WT

description: Library name: Sample 2


title: ChIP THYM H3K9me3 120

description:
Library name: PC count ChIP THYM H3K9me3 120
Competitive PCR product derived from ChIP DNA

value: Thymdine


title: 4Cseq_bulk_GBM8_Pool_of_siRNAs_HOTAIRM1_viewpoint

description: Library name: Sample 7

value: low-passage glioma-initiating stem-like cells


title: control-GFP 2

description: Library name: Sample 8


city: London

first: Harry

last: Pink

address: Innovation and Translation Hub, 84 Wood Lane,

country: United Kingdom

institute: Mitra Bio

description:
Library name: M4088
M4088 (subject 119-3 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

data_processing:
Data was processed as recommended here - https://www.twistbioscience.com/sites/default/files/resources/2022-06/DOC-001301_TechNote-AnalyzingTargetedMethylSeqDataUsingTwistHumanMethylPanel-REV1-singles (1).pdf
Assembly: hg38
Supplementary files format and content: Beta methylation values (0-100) returned by methyldakel. Gzipped txt format
Library strategy: EM-seq

source_name: forehead tape-strip

growth_protocol: Genomic DNA extracted from ‘tape-strip’ of forehead

extract_protocol:
Genomic DNA was extracted
Extracted gDNA underwent EM-seq enzymatic conversion and subsequent hybridisation to Twist Human Methylome 4M CpG panel - https://www.twistbioscience.com/sites/default/files/resources/2022-06/covered_targets_Twist_Methylome_hg38_annotated_collapsed.bed

treatment_protocol: Participants were exposed to treatment with 1940-nm non-ablative fractional laser (NAFL)

tag: subject id

tag: timepoint

value: 3 Month Follow Up

value: Untreated

tag: age

value: forehead tape-strip

tag: gender

value: Female


title: Stool-4w-WT-3-737

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Assembly: The training method of the QIIME2 classifier follows these steps: - Extract all the read datafrom a reference database, in our report, SILVA version 138 with 99% similarity was used.
Supplementary files format and content: File name = abs-abund-table-7 (all 90 samples); Format = excel (.xlsx); Content = raw counts of sequencing reads for the bacteria strain
Supplementary files format and content: File name = rel-table-7 (all 90 samples); Format = excel (.xlsx); Content=relative abundance of sequencing reads for the bacteria strain

source_name: Feces

extract_protocol:
Fecalpellets werecollected asepticallyand placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit protocol.
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)
16S ribosomal RNA (rRNA) gene sequencing

value: Feces

tag: time

value: 4 weeks old


title: control-GFP 1

description: Library name: Sample 7


title: ChIP THYM H3K36me2 120

description:
Library name: PC count ChIP THYM H3K36me2 120
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: Sample 6 WT

description: Library name: Sample 6


title: Sample 12 KO

description: Library name: Sample 12


title: 4Cseq_bulk_GBM8_Pool_of_siRNAs_HOTAIR_viewpoint

description: Library name: Sample 6


title: ChIP THYM K4K20me1 120

description:
Library name: PC count ChIP THYM K4K20me1 120
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma


title: siPRDM16 3

description: Library name: Sample 6


title: Sample 5 WT

description: Library name: Sample 5


title: 4Cseq_bulk_GBM8_Control_siRNA_LINC01116_viewpoint

description: Library name: Sample 5

value: Control siRNA


title: siPRDM16 2

description: Library name: Sample 5

value: Human iPS derived cardiomyocytes


title: ChIP THYM H4K8ac 120

description:
Library name: PC count ChIP THYM H4K8ac 120
Competitive PCR product derived from ChIP DNA

value: carrying HAC 1-20


title: 4Cseq_bulk_GBM8_Control_siRNA_HOXDas2_viewpoint

description: Library name: Sample 4


title: Sample 10 KO

description: Library name: Sample 10


title: ChIP THYM H3K14ac 120

description:
Library name: PC count ChIP THYM H3K14ac 120
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: 4Cseq_bulk_GBM8_Control_siRNA_HOXBas1_viewpoint

description: Library name: Sample 3


title: Sample 3 WT

description: Library name: Sample 3

value: Pancreatic Islets


title: siPRDM16 1

description: Library name: Sample 4


title: 4Cseq_bulk_GBM8_Control_siRNA_HOTAIRM1_viewpoint

description: Library name: Sample 2


title: Sample 9 KO

description: Library name: Sample 9

value: KO


title: ChIP THYM H3K4me2 120

description:
Library name: PC count ChIP THYM H3K4me2 120
Competitive PCR product derived from ChIP DNA


title: ChIP THYM CENPA 120

description:
Library name: PC count ChIP THYM CENPA 120
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: 4Cseq_bulk_GBM8_Control_siRNA_HOTAIR_viewpoint

description: Library name: Sample 1

value: WT


title: Sample 7 KO

description: Library name: Sample 7


title: control 1

description: Library name: Sample 1


title: ChIP H3K9me3 465

description:
Library name: PC count ChIP H3K9me3 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65


title: shYBX1_rep3

city: vancouver

first: Gregg

last: Morin

address: 675 West 10th Ave

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
Aligned to GRCh37-lite, repositioned using Jaguar 1.7.5 using Ensembl 69
Transcripts read counts were computed with summarizeOverlaps R function.
Genes with a read count higher than 10 in at least one sample were included in the analysis.
DESeq2 was used for differential expression analysis and fpkm calculation
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each sample.

growth_protocol: For stable inhibition, shYB-1 (sc-38634-V, Santa Cruz) or shScr (sc-108080) lentiviral particles were used.

extract_protocol:
To prepare cell suspensions from tumors, the tissue was minced with a scalpel, incubated at 37 °C in DMEM/Ham’s F12 media supplemented with 5% FBS and 300 U/ml collagenase and 100 U/ml hyaluronidase for 1 to 2 hours with periodic vortexing, washed with HF, and treated with 2.5 mg/ml trypsin with 1 mM EDTA and 5 mg/ml dispase with 100 μg/ml DNaseI. Human cells were sorted after staining with anti-human specific antibodies directed against EpCAM and CD298 with simultaneous depletion of mouse cells stained with anti-mouse-specific antibodies directed against CD45 and CD31.
The paired-end sequencing library was prepared following BC Cancer Genome Sciences Centre’s strand-specific, plate-based library construction protocol on a Microlab NIMBUS robot (Hamilton Robotics, USA). Briefly, the sheared cDNA was subject to end-repair and phosphorylation in a single reaction using an enzyme premix (NEB) containing T4 DNA polymerase, Klenow DNA Polymerase and T4 polynucleotide kinase, incubated at 20oC for 30 minutes. Repaired cDNA was purified in 96-well format using PCR Clean DX beads (Aline Biosciences, USA), and 3’ A-tailed (adenylation) using Klenow fragment (3’ to 5’ exo minus) and incubation at 37oC for 30 minutes prior to enzyme heat inactivation. Illumina PE adapters were ligated at 20oC for 15 minutes. The adapter-ligated products were purified using PCR Clean DX beads, then digested with 3µL of USERTM enzyme (1U/µL, NEB) at 37oC for 15 minutes followed immediately by 13 cycles of indexed PCR using Phusion DNA Polymerase (Thermo Fisher Scientific Inc. USA) and Illumina’s PE primer set. PCR parameters: 98˚C for 1 minute followed by 13 cycles of 98˚C  15 seconds, 65˚C  30 seconds and 72˚C  30 seconds, and then 72˚C  5 minutes. The PCR products were purified and size-selected using a 1:1 PCR Clean DX beads-to-sample ratio (twice), and the eluted DNA quality was assessed and quantified using the Caliper LabChip GX DNA High Sensitivity assay (PerkinElmer) and the Quant-iT dsDNA high sensitivity assay (ThermoFisher Scientific). Libraries were normalized and pooled and the final concentration of the pooled library was double checked and determined by Qubit dsDNA HS Assay Kit using a Qubit fluorometer (ThermoFisher Scientific).

tag: cell source

value: tumor


title: Sample 1 WT

description: Library name: Sample 1


title: A375R_WT_III

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

description: Library name: Sample 9

data_processing:
Normalization and differential expression analyses were conducted using DESeq2 R package (v1.36.0)
The similarity between samples was evaluated within DESeq2 package using a euclidean distance matrix (shown in a heatmap with a clustering dendogram) and a principal component analysis (PCA).The latter is drawn from the most variable genes (50, 500, 1000, 2000, 5000, 10000 genes)
The threshold for significantly differentially expressed genes is determined by two factors: FDR adjusted p-value ≤ 0.05 and the ‘base-mean independent filtering’ threshold, which is calculated by the DESeq2 algorithm for each comparison
FDR was calculated using the default approach of DESeq2, Benjamini-Hochberg (BH). Since in both experiments, no major batch effect was indicated, a simple single-factor model was applied and lists of DEGs were created for all the possible contrasts
Assembly: GRCh38.109
Supplementary files format and content: tab-deliminated text file with normalized counts

extract_protocol:
RNA extraction was performed using MACHEREY-NAGEL NucleoSpin RNA, Mini kit for RNA purification
15 RNA-seq libraries were constructed simultaneously using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7760), according to the manufacturer protocol.


title: shYBX1_rep2


title: A375R_WT_II

description: Library name: Sample 8


title: Sample 48 Experimental

description:
Library name: Sample 48
S8

data_processing:
The reads are trimmed for adapters and polyX tails using fastp.
The gene count table is generated by aligning reads to the mouse transcriptome (Ensembl version 113) using kallisto and converting transcript counts to gene counts using tximport.
Assembly: GRCm39
Supplementary files format and content: CSV, gene counts

molecule: polyA RNA

extract_protocol:
Trizol with Qiagen columns
PolyA Selection followed by library construction using NEBNext Ultra II Directional kit

value: alpha cell

value: Yy1-overexpressing plasimd


title: ChIP K4K20me1 465

description:
Library name: PC count ChIP K4K20me1 465
Competitive PCR product derived from ChIP DNA


title: shYBX1_rep1


title: ChIP H4K8ac 465

description:
Library name: PC count ChIP H4K8ac 465
Competitive PCR product derived from ChIP DNA


title: Sample 46 Experimental

description:
Library name: Sample 46
S6


title: A375R_VHL_10um_2hr_III

description: Library name: Sample 6


title: ChIP H3K14ac 465

description:
Library name: PC count ChIP H3K14ac 465
Competitive PCR product derived from ChIP DNA


title: shScr_rep3

value: control


title: Sample 45 Experimental

description:
Library name: Sample 45
S5


title: shScr_rep2


title: ChIP H3K4me2 465

description:
Library name: PC count ChIP H3K4me2 465
Competitive PCR product derived from ChIP DNA


title: A375R_VHL_10um_2hr_II

description: Library name: Sample 5


title: Sample 34 Control

description:
Library name: Sample 34
S4

value: empty plasimd


title: ChIP H3K9me3 120

description:
Library name: PC count ChIP H3K9me3 120
Competitive PCR product derived from ChIP DNA


title: shScr_rep1


title: A375R_L3linker_1_10um_2hr_III

description: Library name: Sample 3


title: ChIP H3K36me2 120

description:
Library name: PC count ChIP H3K36me2 120
Competitive PCR product derived from ChIP DNA


title: Sample 33 Control

description:
Library name: Sample 33
S3


title: A375R_L3linker_1_10um_2hr_II

description: Library name: Sample 2


title: ChIP K4K20me1 120

description:
Library name: PC count ChIP K4K20me1 120
Competitive PCR product derived from ChIP DNA


title: INTS12_KO_-DOX_REP2

description:
Library name: INTS12_KO_REP2_eNET-seq
eNET-seq

data_processing:
Adapters were trimmed using cutadapt (v2.3) and reads were aligned to the hg38 human genome using Bowtie2 (v2.3.2). PCR duplicates were removed using UMI-tools (v0.5.4) and read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 3’ end. Reads were filtered to only include those with a mapping quality score >=10, and to remove reads that did not align within 5 kb of a protein coding gene, or that aligned to a snoRNA gene.
Read counts were normalized by library size and the size of the bin.
Assembly: Hg38
Supplementary files format and content: bigwig files for forward and reverse strands

extract_protocol:
As previously described in Fong et al., 2022
As previously described in Fong et al., 2022

value: HEK293 FlpIn-TREx


title: Sample 31 Control

description:
Library name: Sample 31
S1


title: INTS12_KO_-DOX_REP1

description:
Library name: INTS12_KO_REP1_eNET-seq
eNET-seq


title: miR-30c, mice 5

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

description: Library name: M5

data_processing:
Raw data in fastq format were processed by Novogene using their in-house Perl scripts  to obtain clean reads by removing adapter sequences, reads with poly-N, and low-quality reads.
Trimmed sequence reads were mapped to GRCh37/hg19 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm39
Supplementary files format and content: gene_count.xlsx

source_name: Liver

growth_protocol: All mice were on Wesstern diet thorughout the study

extract_protocol:
Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific, # 15596018) following manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: One grou of mice received C2 injection and the other received miR-30c.

value: Liver


title: SH3_RPF_rep3

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

country: Germany

institute: Deutsches Krebsforschungszentrum

data_processing:
For ribosome footprint samples (RPF), adapter sequences (AGATCGGAAGAGCACACGTCT) were removed using the FASTX-toolkit v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/), retaining only reads of at least 20 nt length.
Both input (IN) and RPF sequences were aligned to rRNA and tRNA sequences with bowtie v1.2.2 (Langmead et al., Genome Biology 2009), to remove contaminations. Only reads that did not align in this step were further aligned to the basic set of Gencode V38 (wgEncodeGencodeBasicV38) as downloaded from the UCSC Genome Browser, using bowtie v1.2.2, allowing a maximum of 2 mismatches and reporting all alignments in the best stratum (-a --best --strata -v 2).
Read counts were summarized at the gene level by counting the number of all reads that specifically align to open reading frames on isoforms of the same gene (as defined by a common gene symbol). For the start codon, a P-site offset of -12 nt was assumed, and for the stop codon an offset of -15 nt respective to the 5'end of the read. For RPFs, only reads of length 26 to 30 were considered, because these fragments sizes display the best periodicity.
Read counts were normalized with DESeq2 (Love et al., Genome Biology 2014) using the median of ratios method. Statistics for changes in IN, RPFs and ribosome density (RD) in knockdown (SH2, SH3) versus control cells (SC) was performed with DESeq2, applying a Likelihood Ratio Test (LRT) for changes in RD.
In addition, the alignments were used to analyze codon usage using RiboVIEW (Legrand et al., NAR 2020), after filtering them to retain only reads aligning to isoforms of one specific gene.
Assembly: wgEncodeGencodeBasicV38
Supplementary files format and content: The file DESeq2_output_26to30.csv contains read counts per gene and normalized read counts per gene as produced by DESeq2.

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) enriched 10% foetal bovine serum, 1% penicillin/streptomycin antibiotics and 0.1% human insulin.

extract_protocol:
MDA-MB-231 cells representing control and KD cells were cultured for 96 h in a puromycin medium (1 µg/ml). After that, the medium was changed with fresh, complete media. The following day, cells were treated with cycloheximide (CHX) (100 µg/ml) for 5 min and washed twice with cold 1X PBS containing CHX (100 µg/ml). Cells were further lysed in polysome lysis buffer (20mM Tris-HCl, pH 7.4, 5 mM MgCl2, 150 mM NaCl, 1% triton X-100) supplemented with 100 µg/ml cycloheximide, 1X complete protease inhibitors (complete EDTA-free, Roche), and 200U/ml of RiboLock RNase Inhibitor (ThemoScientific™). The lysates were tumbled for 10 minutes and then centrifuged at 10000 x g for 10 minutes at 4°C. Cleared lysates were normalised according to NanoDrop™ Lite Spectrophotometer (ThermoScientific™) measurements and layered on sucrose gradients (15-45% w/v) priorly prepared using Gradient Master (BioComp Instruments). The polyallomer tubes containing the sucrose gradients and the lysate were centrifuged at 39000xg for 2h at 4°C in an ultracentrifuge SW60 Ti rotor head (Beckmann). Fractions of 280 µl were collected using Gilson Fraction FC-203B Collector in tubes containing 300 µl Solution II (10 mM Tris-HCl pH 7.5; 350 mM NaCl; 10 mM EDTA; 1% SDS; 42% Urea) while continuously measuring the absorbance (A260) using the Triax™ flow cell (BioComp Instruments).
For each sample, the absorbance of the lysate was measured with a NanoDrop spectrophotometer, and 10 µg of RNA was stored as input cytoplasmic RNA. The remaining lysate was treated with 4 U of DNase I (ThemoScientific™) and 800 U of RNase I (Ambion) for 45 min at R/T with gentle shaking. 800 U of RNasin ribonuclease inhibitor (Promega) was added to quench the reaction, and the samples were run on a 17.5–50% sucrose gradient to isolate monosomes. After separation through ultracentrifugation, the gradients were fractionated using an ISCO gradient fractionator (Brandel) and the fractions were collected in 300 µl of Solution II (see polysome profiling section). RNA from the monosome containing fraction and RNA Input samples were isolated using Phenol:Chloroform:Isoamyl alcohol (25:24:1). The RNA was quantified using a 2200 Agilent R6K ScreenTape station. Monosome-protected RNA fragments were dephosphorylated using T4 polynucleotide kinase (PNK) (Takara), and subsequently RNA was extracted using acid-phenol. Further, RNA was separated in a 15% polyacrylamide TBE-urea gel and footprint fragments 20-30 nucleotides (nt) in length were isolated from the gel. Sequencing libraries were prepared according to the protocol of the NEB NEXT Small RNA Library Prep Set for Illumina (Multiplex Compatible) E7330 kit. The cytoplasmic RNA (RNA Input) was sequenced using Illumina HiSeq V4 SR 50, while the footprint library used small RNA Seq-HiSeq V4 SR 50.

treatment_protocol: Two short hairpin RNAs (shRNA) targeting fibrillarin mRNA (shRNA_fibrillarin_1 and shRNA_fibrillarin_2, table S1), later referred to as knockdown 1 and 2 (KD1 and KD2), were cloned in pLKO.1-Puro and pLKO.1-Hygro (Addgene #24150) following Addgene’s recommendations with few changes. Briefly, plasmids were digested using AgeI and EcoRI restriction enzymes (Anza, Invitrogen). shRNAs oligos were annealed and ligated into the pLKO.1 backbone vector. Cloning was validated by Sanger sequencing. Lentiviral particles were generated by transfecting HEK-293T cells with lentiviral plasmids pLKO.1-Puro/Hygro containing shRNA or Scramble (Scr) control, the pCMV-dR8.2 packaging and pCMV-VSV-G helper plasmids using jet-PEI (Polyplus) as per the manufacturer’s instructions. Lentiviral particles were collected after 48 and 72 hours of incubation and concentrated using Amicon Ultra-15 Centrifugal Filter Units (Merck). MDA-MB-231 cells were transduced with the lentiviral particles in media supplemented with Polybrene (8 µg/ml). After being incubated with the virus for 48 hours, cells were selected with puromycin 1 µg/ml or 500 µg/ml hygromycin for 96 hours, depending on the downstream experiments.

value: breast carcinoma


title: ChIP H3K14ac 120

description:
Library name: PC count ChIP H3K14ac 120
Competitive PCR product derived from ChIP DNA

value: Connective tissue

value: Fibrosarcoma


title: INTS12_KO_+DOX_REP2

description:
Library name: INTS12_WT_REP2_eNET-seq
eNET-seq


title: miR-30c, mice 4

description: Library name: M4


title: SH3_RPF_rep2


title: miR-30c, mice 3

description: Library name: M3


title: SH3_RPF_rep1


title: INTS12_45_R2

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR (Dobin et al, 2012) / RSEM (B et al 2011) option against human genome assembly GRCh38 and Ensembl release 104 transcript annotations.  Data were simultaneously aligned against Saccharomyces cerevisiae R64-1-1 cdna sequences (Ensembl 104) using the “--additional_fasta” flag in order to quantify the yeast spike-in reads
Reads Per Kilobase per Million mapped reads (RPKM) scaled BigWig files were generated by converting BAM files to bedGraph format using Deeptools’ bamCoverage function for each strand in turn using the options “--normalizeUsing RPKM --exactScaling –effectiveGenomeSize (Ramirez et al., 2014).
Assembly: GRCh38
Supplementary files format and content: Per-sample, strand-specific, RPKM normalised coverage bigwig files.

source_name: HEK293 FlpIn TREx

growth_protocol: Flp-In TREx HEK293 cells were cultured in high glucose DMEM supplemented with 10% v/v FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine and at 37 oC with 5% CO2 and routinely passaged 2-3 times a week.

extract_protocol:
TTchem-seq RNA preparation was performed as previously described (Gregersen et al., 2020).
TTchem-seq libraries were prepared using the KAPA RNA HyperPrep Kit (Roche, 08098093702) with the fragmentation step omitted. 75 ng of nascent RNA was denatured at 65°C for 5 min. The rest of the procedure was performed following manufacturer’s instructions, except that two SPRI bead purifications (Beckman Coulter, A63881) were carried out, with a bead-to-sample volume ratio of 0.95x and 1x respectively.

treatment_protocol: Cells were treated with 100μM 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) in DMSO for 2hrs. DRB was washed-out by replacement of DRB-containing media with normal media. For the given timepoints (15', 30', 45'), 1mM 4-thiouridine (4SU) was added directly to the to the medium 10' before the specified timepoint. Reactions were quenched by removal of media and addition of TRIzol to the cells. For "nonDRB" samples, no treatments were carried out.

value: HEK293 FlpIn TREx

value: INTS12 KO

value: 2hrs 100uM DRB; DRB wash-out; 45' incubation


title: SH3_IN_rep3


title: ChIP CENPA 36

description:
Library name: PC count ChIP CENPA 36
Competitive PCR product derived from ChIP DNA

value: carrying HAC 3-6


title: INTS12_45_R1


title: SH3_IN_rep2


title: ChIP CENPA 465

description:
Library name: PC count ChIP CENPA 465
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: INTS12_30_R2

value: 2hrs 100uM DRB; DRB wash-out; 30' incubation


title: C2, mice 5

description: Library name: C5


title: SH3_IN_rep1


title: miR-30c, mice 1

description: Library name: M1


title: ChIP CENPA 42

description:
Library name: PC count ChIP CENPA 42
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-2


title: INTS12_30_R1


title: C2, mice 4

description: Library name: C4


title: SH2_RPF_rep3


title: control 3

description: Library name: Sample 3

value: Human iPS derived cardiomyocytes


title: control 2

description: Library name: Sample 2


title: ChIP CENPA 18

description:
Library name: PC count ChIP CENPA 18
Competitive PCR product derived from ChIP DNA

value: carrying HAC 1-8


title: INTS12_15_R2

value: 2hrs 100uM DRB; DRB wash-out; 15' incubation


title: Sample 47 Experimental

description:
Library name: Sample 47
S7

value: alpha cell

value: Yy1-overexpressing plasimd


title: ChIP H3K36me2 465

description:
Library name: PC count ChIP H3K36me2 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65


title: SH2_RPF_rep2


title: C2, mice 3

description: Library name: C3

value: Liver


title: ChIP CENPA 120

description:
Library name: PC count ChIP CENPA 120
Competitive PCR product derived from ChIP DNA

value: carrying HAC 1-20


title: A375R_WT_I

description: Library name: Sample 7


title: INTS12_15_R1


title: shYBX1_cell


title: A375R_VHL_10um_2hr_I

description: Library name: Sample 4


title: SH2_RPF_rep1

value: breast carcinoma


title: C2, mice 2

description: Library name: C2


title: HAC 4-65 cells, RT plus

description:
Library name: PC count RNA 465p
Competitive PCR product derived from total RNA

extract_protocol:
RNA was harvested using Trizol (TAKARA), and 1 µg of total RNA was used for reverse transcription.
Then 100 ng of the cDNA was used for competitive PCR to the construction of sequencing library.

value: Connective tissue

value: Fibrosarcoma

value: Reverse transcribed


title: INTS12_nonDRB_R2

value: HEK293 FlpIn TREx

value: INTS12 KO


title: C2, mice 1

description: Library name: C1


title: SH2_IN_rep3


title: HAC 4-65 cells, RT minus

description:
Library name: PC count RNA 465m
Competitive PCR product derived from total RNA

value: No reverse transcription


title: shScr_cell

value: control


title: INTS12_nonDRB_R1


title: Sample 32 Control

description:
Library name: Sample 32
S2

value: empty plasimd


title: Treatment sample 4

city: Wuhan

first: Nannan

last: WANG

state: Hubei Province

address: No. 1, Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description:
Library name: T_4
Column name in expression matrix: T_4; treatment sample cultured with 2 μM A485.

data_processing:
Raw reads were filtered using SOAPnuke v1.5.6 with parameters: -n 0.01 -l 20 -q 0.4 --adaMR 0.25 --polyX 50.
Clean reads were aligned to the Mus musculus reference genome GRCm38.p6 (NCBI GCF_000001635.26) using HISAT2 v2.2.1.
Gene expression levels, including FPKM, TPM, raw read counts, and normalized read counts, were calculated using RSEM v1.2.28.
Differential expression analysis between CK and T groups was performed using DESeq2 v1.40.2 with a q-value threshold of 0.05.
Assembly: Mus musculus GRCm38.p6, NCBI GCF_000001635.26
Supplementary files format and content: Tab-delimited text file containing gene-level expression values and differential expression results, including FPKM, TPM, raw read counts, normalized read counts, average expression values, log2 fold change, P value, Q value, and gene annotation information for all samples.

source_name: Morula

extract_protocol:
Morula-stage embryos were briefly incubated in acid Tyrode’s solution to remove the zona pellucida and then washed thoroughly in PBS. Three embryos were pooled as one biological replicate. Embryo lysis, reverse transcription, cDNA preamplification, and purification were performed using the SuperScript™ IV Single Cell/Low Input cDNA PreAmp Kit (Cat. No. 11752480, Thermo Fisher Scientific) according to the manufacturer’s instructions.
Purified amplified cDNA products were processed for library construction with a transposase-based method, followed by high-throughput sequencing.

treatment_protocol: For the control group, embryos were cultured in KSOM containing 0.1% DMSO from the 4-cell stage to the blastocyst stage. For the treatment group, embryos were cultured in KSOM containing 2 μM A485 from the 4-cell stage to the blastocyst stage.

value: Morula

value: wild-type


title: SH2_IN_rep2


title: Ctrl_45_R2

value: WT

value: 2hrs 100uM DRB; DRB wash-out; 45' incubation


title: HAC 1-20 cells, RT plus

description:
Library name: PC count RNA 120p
Competitive PCR product derived from total RNA


title: Treatment sample 3

description:
Library name: T_3
Column name in expression matrix: T_3; treatment sample cultured with 2 μM A485.


title: SH2_IN_rep1


title: HAC 1-20 cells, RT minus

description:
Library name: PC count RNA 120m
Competitive PCR product derived from total RNA


title: Ctrl_45_R1


title: ChIP H4K8ac 120

description:
Library name: PC count ChIP H4K8ac 120
Competitive PCR product derived from ChIP DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at RT. After quenching and hypotonic treatment, then cells were sonicated using a picoruptor 2 apparatus (Diagenode).
A DNA pool of triplicate ChIP was prepared and 10 μl of the pool was used for competitive PCR to the construction of sequencing library.


title: Treatment sample 2

description:
Library name: T_2
Column name in expression matrix: T_2; treatment sample cultured with 2 μM A485.


title: SC_RPF_rep3

value: SC


title: genome DNA  449

description:
Library name: PC count  genome DNA  449
Competitive PCR product derived from genomic DNA

data_processing:
Fastq files were generated by Miseq base calling.
Sequencing reads were trimmed with cutadapt 4.0 using Python 3.9.13.
Trimmed reads were matched against the indexed list of the position code DNA using bowtie.
The number of reads for each the position code was obtained using samtools idxstats (1.11).
Note that to minimize deviations in counts at each position caused by competitive PCR, the ratio of position code DNA in genomic DNA was normalized by the ratio of position code DNA in the original input BAC plasmid.
Assembly: The index list of the position code DNA (See also supplementary Inofrmation)
Supplementary files format and content: Tab-delimited text file includes raw counts for each the position code.

growth_protocol: Human HT1080 and derived cells were cultured in the DMEM Glutamax I (10569010, Gibco) supplemented with the 10% tet-system approved Fetal Bovine Serum (631101, TAKARA) at 37˚ C and 5% CO2. The E. coli (DH10B)-derived strain carrying the BAC was cultured at 30°C.

extract_protocol:
Genomic DNA was extracted from each cell line carrying the human artificial chromosome using Genomic tip 100 (Qiagen). BAC plasmid was also prepared using Large construction kit (Qiagen).
Then 100 ng of the genomic DNA or 1 ng of BAC plasmid DNA was used for competitive PCR to the construction of sequencing library.

treatment_protocol: A hundred ng of the genomic or BAC plasmid DNA was used for competitive PCR to the construction of sequencing library.

value: carrying HAC 4-49


title: A375R_L3linker_1_10um_2hr_I

description: Library name: Sample 1


title: Ctrl_30_R2

value: 2hrs 100uM DRB; DRB wash-out; 30' incubation


title: Treatment sample 1

description:
Library name: T_1
Column name in expression matrix: T_1; treatment sample cultured with 2 μM A485.


title: SC_RPF_rep2


title: genome DNA  36

description:
Library name: PC count  genome DNA  36
Competitive PCR product derived from genomic DNA

value: carrying HAC 3-6


title: Ctrl_30_R1


title: Control sample 4

description:
Library name: CK_4
Column name in expression matrix: CK_4; control sample cultured with 0.1% DMSO.

value: 0.1% DMSO


title: SC_RPF_rep1

value: breast carcinoma


title: Ctrl_15_R2

value: 2hrs 100uM DRB; DRB wash-out; 15' incubation


title: genome DNA  465

description:
Library name: PC count  genome DNA  465
Competitive PCR product derived from genomic DNA

value: Connective tissue

value: Fibrosarcoma

value: carrying HAC 4-65


title: Control sample 3

description:
Library name: CK_3
Column name in expression matrix: CK_3; control sample cultured with 0.1% DMSO.


title: SC_IN_rep3


title: ChIP H3K4me2 120

description:
Library name: PC count ChIP H3K4me2 120
Competitive PCR product derived from ChIP DNA

data_processing:
Fastq files were generated by Miseq base calling.
Sequencing reads were trimmed with cutadapt 4.0 using Python 3.9.13.
Trimmed reads were matched against the indexed list of the position code DNA using bowtie.
The number of reads for each the position code was obtained using samtools idxstats (1.11).
Assembly: The index list of the position code DNA (See also supplementary Inofrmation)
Supplementary files format and content: Tab-delimited text file includes raw counts for each the position code.

value: carrying HAC 1-20


title: INTS12_KO_+DOX_REP1

description:
Library name: INTS12_WT_REP1_eNET-seq
eNET-seq

value: HEK293 FlpIn-TREx


title: genome DNA  42

description:
Library name: PC count  genome DNA  42
Competitive PCR product derived from genomic DNA

value: carrying HAC 4-2


title: Control sample 2

description:
Library name: CK_2
Column name in expression matrix: CK_2; control sample cultured with 0.1% DMSO.

value: Morula


title: Ctrl_15_R1

value: HEK293 FlpIn TREx


title: Ctrl_nonDRB_R2

value: WT


title: genome DNA  18

description:
Library name: PC count  genome DNA  18
Competitive PCR product derived from genomic DNA

value: carrying HAC 1-8


title: SC_IN_rep1

value: SC


title: genome DNA 120

description:
Library name: PC count genome DNA 120
Competitive PCR product derived from genomic DNA


title: SC_IN_rep2


title: Ctrl_nonDRB_R1


title: isoflurane treatment; male M4

status: Public on Jul 07 2026

city: Philadelphia

first: Allan

middle: I

last: Pack

address: 125 South 31st St

institute: University of Pennsylvania

description:
Library name: iso-M4
10x Genomics 3′ Reagent kit v3

data_processing:
Data were processed using the Cellranger pipeline (10x genomics, v.6.1.2) for de-multiplexing and alignment of sequencing reads to the mm10 transcriptome with the “include introns” parameter and creating the feature-barcode matrices.
Assembly: Mouse mm10
Supplementary files format and content: barcodes, features, and matrix for each sample separated into inhibitory/excitatory neuronal cells and nonneuronal cells

source_name: brain

extract_protocol:
Brains were harvested following cervical dislocation and flash frozen on dry ice. Preoptic area of hypothalamus (POA) was dissected from frozen tissues. Nuclei were isolated from the dissected POA tissues using Minute Single Nucleus Isolation Kit for Neuronal Tissues/Cells (Invent Biotechnologies, Inc., BN-020). The isolated nuclei were resuspended in 2%BSA solution (in 1xPBS with 0.2U/ul of Protector RNase inhibitor) to a concentration of 900–1200 nuclei/μL and were loaded onto the 10x Genomics microfluidic device at maximum capacity for a target capture of ~10,000 nuclei per sample.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent kit v3 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run. Sequencing for each library targeted 20,000 mean reads per nuclei.

value: brain

tag: Sex

value: male

value: isoflurane


title: isoflurane treatment; male M5

description:
Library name: iso-M5
10x Genomics 3′ Reagent kit v3


title: isoflurane treatment; male M3

description:
Library name: iso-M3
10x Genomics 3′ Reagent kit v3


title: ChIP CENPA 449

description:
Library name: PC count ChIP CENPA 449
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-49

value: CENP-A (A1, Masumoto Lab.)


title: isoflurane treatment; male M2

description:
Library name: iso-M2
10x Genomics 3′ Reagent kit v3


title: isoflurane treatment; male M1

description:
Library name: iso-M1
10x Genomics 3′ Reagent kit v3


title: isoflurane treatment; female F5

description:
Library name: iso-F5
10x Genomics 3′ Reagent kit v3

value: female


title: isoflurane treatment; female F3

description:
Library name: iso-F3
10x Genomics 3′ Reagent kit v3


title: isoflurane treatment; female F4

description:
Library name: iso-F4
10x Genomics 3′ Reagent kit v3


title: miR-30c, mice 2

description: Library name: M2

value: Liver


title: isoflurane treatment; female F2

description:
Library name: iso-F2
10x Genomics 3′ Reagent kit v3


title: isoflurane treatment; female F1

description:
Library name: iso-F1
10x Genomics 3′ Reagent kit v3


title: Control sample 1

description:
Library name: CK_1
Column name in expression matrix: CK_1; control sample cultured with 0.1% DMSO.

value: wild-type

value: 0.1% DMSO


title: OxyControl; male M4

description:
Library name: Control-M4
10x Genomics 3′ Reagent kit v3

value: Oxygen


title: OxyControl; male M5

description:
Library name: Control-M5
10x Genomics 3′ Reagent kit v3


title: OxyControl; male M3

description:
Library name: Control-M3
10x Genomics 3′ Reagent kit v3


title: OxyControl; male M2

description:
Library name: Control-M2
10x Genomics 3′ Reagent kit v3


title: OxyControl; male M1

description:
Library name: Control-M1
10x Genomics 3′ Reagent kit v3


title: OxyControl; female F4

description:
Library name: Control-F4
10x Genomics 3′ Reagent kit v3


title: OxyControl; female F3

description:
Library name: Control-F3
10x Genomics 3′ Reagent kit v3


title: OxyControl; female F5

description:
Library name: Control-F5
10x Genomics 3′ Reagent kit v3


title: OxyControl; female F1

description:
Library name: Control-F1
10x Genomics 3′ Reagent kit v3


first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Library name: I33H9_uterus_CtrachomatisL2_primaryD15_TCR

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Library strategy: TCR-seq

source_name: uterus

extract_protocol:
Single-cell suspensions were prepared from each organ of 6-week-old male and female wild-type C57BL/6J mice using collagenase IV, DNAse I, or mechanical dissociation alone. Target cell populations included all T cells and splenocytes, gated as CD45+ CD3e+ or CD45+ by flow cytometry.
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

treatment_protocol: Single-cell suspensions from the uterus were prepared using collagenase XI and DNase I. TCRβ/γδ+ T cells were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

value: uterus

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: T cells in the uterus during C. trachomatis infections (D and L2)

tag: lab

value: Starnbach

tag: organism name

tag: strain

tag: genetics

value: NR23.4 and NR1 > Thy1.1 (B6.PL-Thy1a/CyJ)

tag: age weeks

tag: pool of_mice

value: FALSE

tag: infection agent

value: Chlamydia trachomatis L2 (434/Bu)

tag: infection dose

value: 5x10E6 IFU

tag: infection mode

value: transcervical

value: 15 dpi primary

tag: prep description

value: collagenase XI, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T including NR23.4 and NR1

tag: gating strategy

value: CD45+ TCRb/gd+

tag: sample comments

value: 1% transgenic cells NR23.4 (CD45.2+ Thy1.2+ GFP-) (CD8) and NR1 (CD45.2+ Thy1.1+ GFP+) (CD4) 250x10E3 NR23.4 and 250x10E3 NR1, intravenous, 1 day before infection; DEPO at d -7 and d21-- 2.5mg medroxyprogesterone acetate, PRASCO, subcutaneous injection

value: T cells


title: OxyControl; female F2

description:
Library name: Control-F2
10x Genomics 3′ Reagent kit v3

tag: tissue

value: brain

tag: Sex

value: female

tag: genotype

tag: treatment


description: Library name: I33H9_uterus_CtrachomatisL2_primaryD15_GEX

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.

value: uterus

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: timepoint

tag: cell type


description: Library name: I33H9_uterus_CtrachomatisL2_primaryD15_FBC

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Library strategy: CITE-seq

value: TRUE

tag: genetics

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: infection mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells


description: Library name: I33H8_uterus_CtrachomatisL2_primaryD5_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: T cells in the uterus during C. trachomatis infections (D and L2)

tag: Sex

value: 5 dpi primary

tag: gating strategy

tag: sample comments


description: Library name: I33H8_uterus_CtrachomatisL2_primaryD5_GEX

tag: exp name

tag: lab

value: Starnbach

tag: organism name

tag: strain

tag: genetics

value: NR23.4 and NR1 > Thy1.1 (B6.PL-Thy1a/CyJ)

tag: age weeks

tag: timepoint

tag: cell type


description: Library name: I33H7_uterus_CtrachomatisD_secondaryD5_TCR

tag: pool of_mice

value: FALSE

tag: infection agent

value: Chlamydia trachomatis D (UW-3/Cs)

tag: infection dose

value: 5x10E6 IFU  at day 0 (primary) and day 28 (challenge)

tag: infection mode

value: 5 dpi secondary

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells


description: Library name: I33H7_uterus_CtrachomatisD_secondaryD5_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: Sex

value: transcervical

value: collagenase XI, DNAse I

tag: gating strategy

tag: sample comments


description: Library name: I33H7_uterus_CtrachomatisD_secondaryD5_FBC

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: age weeks

tag: timepoint

value: all T including NR23.4 and NR1

value: CD45+ TCRb/gd+

tag: cell type


description: Library name: I33H8_uterus_CtrachomatisL2_primaryD5_FBC

tag: pool of_mice

tag: infection agent

value: Chlamydia trachomatis L2 (434/Bu)

tag: infection dose

value: 5x10E6 IFU

tag: infection mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: 1% transgenic cells NR23.4 (CD45.2+ Thy1.2+ GFP-) (CD8) and NR1 (CD45.2+ Thy1.1+ GFP+) (CD4) 250x10E3 NR23.4 and 250x10E3 NR1, intravenous, 1 day before infection; DEPO at d -7 and d21-- 2.5mg medroxyprogesterone acetate, PRASCO, subcutaneous injection

value: T cells


description: Library name: I33H6_uterus_CtrachomatisD_secondaryD3_TCR

tag: tissue

value: uterus

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: Sex

value: female

value: 3 dpi secondary

tag: gating strategy

tag: sample comments


description: Library name: I33H6_uterus_CtrachomatisD_secondaryD3_GEX

tag: exp name

value: T cells in the uterus during C. trachomatis infections (D and L2)

tag: lab

value: Starnbach

tag: organism name

tag: strain

tag: genetics

value: NR23.4 and NR1 > Thy1.1 (B6.PL-Thy1a/CyJ)

tag: age weeks

tag: timepoint

tag: cell type


description: Library name: I33H6_uterus_CtrachomatisD_secondaryD3_FBC

tag: pool of_mice

value: FALSE

tag: infection agent

value: Chlamydia trachomatis D (UW-3/Cs)

tag: infection dose

value: 5x10E6 IFU  at day 0 (primary) and day 28 (challenge)

tag: infection mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells


description: Library name: I33H5_uterus_CtrachomatisD_primaryD15_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: Sex

value: transcervical

value: 15 dpi primary

value: collagenase XI, DNAse I

tag: gating strategy

tag: sample comments


description: Library name: I33H5_uterus_CtrachomatisD_primaryD15_FBC

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: age weeks

tag: timepoint

value: all T including NR23.4 and NR1

value: CD45+ TCRb/gd+

tag: cell type


description: Library name: I33H4_uterus_CtrachomatisD_primaryD5_TCR

tag: pool of_mice

tag: infection agent

tag: infection dose

value: 5x10E6 IFU

tag: infection mode

value: 5 dpi primary

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: 1% transgenic cells NR23.4 (CD45.2+ Thy1.2+ GFP-) (CD8) and NR1 (CD45.2+ Thy1.1+ GFP+) (CD4) 250x10E3 NR23.4 and 250x10E3 NR1, intravenous, 1 day before infection; DEPO at d -7 and d21-- 2.5mg medroxyprogesterone acetate, PRASCO, subcutaneous injection


description: Library name: I33H4_uterus_CtrachomatisD_primaryD5_GEX

tag: tissue

value: uterus

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: Sex

tag: gating strategy

tag: sample comments

value: T cells


description: Library name: I33H5_uterus_CtrachomatisD_primaryD15_GEX

tag: exp name

value: T cells in the uterus during C. trachomatis infections (D and L2)

tag: lab

tag: organism name

tag: strain

tag: genetics

value: female

tag: age weeks

tag: timepoint

tag: cell type


title: I33H3_uterus_GEX

description: Library name: I33H3_uterus_GEX

value: Starnbach

value: NR23.4 and NR1 > Thy1.1 (B6.PL-Thy1a/CyJ)

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: 1% transgenic cells NR23.4 (CD45.2+ Thy1.2+ GFP-) (CD8) and NR1 (CD45.2+ Thy1.1+ GFP+) (CD4) 250x10E3 NR23.4 and 250x10E3 NR1, intravenous, 1 day before infection; Mock inoculated with SPG (chalmydia storage media); DEPO at d7 and d21-- 2.5mg medroxyproge


description: Library name: I33H4_uterus_CtrachomatisD_primaryD5_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: infection agent

value: Chlamydia trachomatis D (UW-3/Cs)

tag: infection dose

tag: infection mode


title: I33H3_uterus_FBC

description: Library name: I33H3_uterus_FBC

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: gating strategy

tag: sample comments


title: I33H3_uterus_TCR

description: Library name: I33H3_uterus_TCR

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: cell type


title: I33H2_uterus_TCR

description: Library name: I33H2_uterus_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq


title: I33H2_uterus_GEX

description: Library name: I33H2_uterus_GEX

tag: exp name

tag: lab

tag: organism name

tag: strain


title: I33H2_uterus_FBC

description: Library name: I33H2_uterus_FBC

tag: genetics

tag: Sex

tag: gating strategy

tag: sample comments


description: Library name: I33H10_uterus_CtrachomatisL2_secondaryD5_TCR

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Chlamydia trachomatis L2 (434/Bu)

tag: infection dose

value: 5x10E6 IFU  at day 0 (primary) and day 28 (challenge)

tag: infection mode

value: transcervical

tag: timepoint

value: 5 dpi secondary

tag: prep description

tag: organ


description: Library name: I33H10_uterus_CtrachomatisL2_secondaryD5_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: collagenase XI, DNAse I

tag: organ uberon_id

tag: target cells

value: all T including NR23.4 and NR1

value: CD45+ TCRb/gd+

tag: cell type


description: Library name: I33H10_uterus_CtrachomatisL2_secondaryD5_FBC

value: uterus

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: gating strategy

tag: sample comments

value: 1% transgenic cells NR23.4 (CD45.2+ Thy1.2+ GFP-) (CD8) and NR1 (CD45.2+ Thy1.1+ GFP+) (CD4) 250x10E3 NR23.4 and 250x10E3 NR1, intravenous, 1 day before infection; DEPO at d -7 and d21-- 2.5mg medroxyprogesterone acetate, PRASCO, subcutaneous injection


title: I33H1_spleen_TCR

description: Library name: I33H1_spleen_TCR

source_name: spleen

value: spleen

value: TRUE

value: wt

tag: age weeks

tag: pool of_mice

tag: prep description

value: mechanical dissociation alone

tag: organ

value: splenocytes

value: T cells


title: I33H1_spleen_GEX

description: Library name: I33H1_spleen_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: T cells in the uterus during C. trachomatis infections (D and L2)

value: Starnbach

value: female

value: FALSE


title: I33H1_spleen_FBC

description: Library name: I33H1_spleen_FBC

tag: cite seq

tag: organ uberon_id

tag: target cells

tag: cell type


title: PoH_rep3

city: Guilin

first: lanyu

last: li

address: No. 1 Zhiyuan Road, Lingui District

institute: Guilin Medical University

description:
Library name: PoH3
Fecal sample from mouse treated with PO extract 3 g/kg via oral gavage daily for 3 days followed by APAP 300 mg/kg i.p., biological replicate 3

data_processing:
Raw reads demultiplexed, barcode/primer removed. Paired-end reads merged with FLASH. Quality filtered and chimera removed. OTU/ASV clustering at 97% similarity. Taxonomy assigned with SILVA database.
OTU/ASV abundance table and taxonomy annotations generated as tab-delimited text files.
Assembly: mm10 (GRCm38)
Supplementary files format and content: ASV_abundance_table.txt: tab-delimited text containing ASV counts per sample with integrated taxonomy annotations.
Library strategy: 16S rRNA-seq

source_name: feces

growth_protocol: Male C57BL/6J mice (18-22g) were housed under SPF conditions with a 12-hour light/dark cycle, controlled temperature (22+/-2C) and humidity (50+/-5%), free access to food and water, with one week of acclimatization.

extract_protocol:
Total DNA extracted from fecal samples. V3-V4 region of 16S rRNA gene amplified with primers 341F (CCTAYGGGRBGCASCAG) and 806R (GGACTACNNGGGTATCTAAT).
PCR products purified, quantified, pooled. Libraries constructed and sequenced on Illumina NovaSeq 6000 platform, paired-end 250 bp.

treatment_protocol: Control: distilled water p.o. daily for 3 days. Model: distilled water p.o. daily for 3 days + APAP 300 mg/kg i.p. PoH: PO extract 3 g/kg p.o. daily for 3 days + APAP 300 mg/kg i.p. Fecal samples collected before euthanization.

value: feces

tag: genotype

tag: treatment

value: PO extract 3 g/kg, p.o. daily for 3 days + APAP 300 mg/kg, i.p.


title: PoH_rep4

description:
Library name: PoH4
Fecal sample from mouse treated with PO extract 3 g/kg via oral gavage daily for 3 days followed by APAP 300 mg/kg i.p., biological replicate 4


title: PoH_rep2

description:
Library name: PoH2
Fecal sample from mouse treated with PO extract 3 g/kg via oral gavage daily for 3 days followed by APAP 300 mg/kg i.p., biological replicate 2


title: Model_rep3

description:
Library name: Model3
Fecal sample from mouse treated with distilled water for 3 days followed by APAP 300 mg/kg i.p., biological replicate 3

value: distilled water, p.o. daily for 3 days + APAP 300 mg/kg, i.p.


title: Model_rep4

description:
Library name: Model4
Fecal sample from mouse treated with distilled water for 3 days followed by APAP 300 mg/kg i.p., biological replicate 4


title: Model_rep1

description:
Library name: Model1
Fecal sample from mouse treated with distilled water for 3 days followed by APAP 300 mg/kg i.p., biological replicate 1


title: Model_rep2

description:
Library name: Model2
Fecal sample from mouse treated with distilled water for 3 days followed by APAP 300 mg/kg i.p., biological replicate 2


title: Control_rep2

description:
Library name: Control2
Fecal sample from healthy control mouse treated with distilled water via oral gavage for 3 days, biological replicate 2

value: distilled water, p.o. daily for 3 days


title: Control_rep3

description:
Library name: Control3
Fecal sample from healthy control mouse treated with distilled water via oral gavage for 3 days, biological replicate 3


title: Control_rep4

description:
Library name: Control4
Fecal sample from healthy control mouse treated with distilled water via oral gavage for 3 days, biological replicate 4


title: Control_rep1

description:
Library name: Control1
Fecal sample from healthy control mouse treated with distilled water via oral gavage for 3 days, biological replicate 1


title: DC2.4 dendritic cells, Rb1-treated, biological replicate 2

city: Shanghai

first: Yuxiang

last: Lu

address: 1200 Cailun Road

institute: shanghai university of traditional chinese medicine

description:
Library name: DC2.4_Rb1_2
Column name in processed matrix files: DC2.4_Rb1_2

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality reads.Clean reads were aligned to the Mus musculus reference genome.Gene-level raw read counts were generated for annotated genes.Gene expression levels were normalized and reported as FPKM values.Differential expression and pathway analyses were performed by comparing Rb1-treated DC2.4 cells with vehicle-treated controls.
Assembly: GRCm39/mm39
Supplementary files format and content: gene_count.xlsx: Excel workbook containing gene-level raw read counts for all samples.  gene_fpkm.xlsx: Excel workbook containing gene-level FPKM values for all samples.

growth_protocol: DC2.4 murine dendritic cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 ug/mL streptomycin. Cells were maintained under standard cell culture conditions and used within limited passages.

extract_protocol:
Total RNA was extracted from DC2.4 cells after vehicle or Rb1 treatment. RNA quality and quantity were assessed before RNA-seq library preparation. Please verify and update the exact extraction reagent or kit according to the sequencing report before final GEO submission.
RNA-seq libraries were prepared from total RNA and sequenced using a paired-end strategy on an Illumina platform. Please verify and update the exact library preparation kit, read length, and sequencing configuration according to the sequencing report before final GEO submission.

treatment_protocol: DC2.4 cells were treated with vehicle or ginsenoside Rb1 (10 uM) for 24 h before RNA collection for bulk RNA-seq.

tag: cell line

value: dendritic cell

value: Rb1 10 uM for 24 h

tag: batch

value: biological replicate 2


title: DC2.4 dendritic cells, Rb1-treated, biological replicate 1

description:
Library name: DC2.4_Rb1_1
Column name in processed matrix files: DC2.4_Rb1_1

value: biological replicate 1


title: DC2.4 dendritic cells, vehicle, biological replicate 2

description:
Library name: DC2.4_Vehicle_2
Column name in processed matrix files: DC2.4_Vehicle_2

value: vehicle for 24 h


title: DC2.4 dendritic cells, vehicle, biological replicate 1

description:
Library name: DC2.4_Vehicle_1
Column name in processed matrix files: DC2.4_Vehicle_1


title: Ang II_FI_4

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Sample 12

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl 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.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include Counts for each Sample
Supplementary files format and content: txt files include Counts for each Sample

source_name: ventricular

growth_protocol: The mice were randomly divided into three experimental groups: saline + vehicle, angiotensin II (Ang II) + vehicle, and Ang II + Forsythoside I (FI).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA w as used for the construction of sequencing libraries.
RNA libraries for RNA-seq w ere prepared using SMARTER mRNA-Seq Library Prep Kitfollow ing manufacturer's protocols.

treatment_protocol: Cardiac hypertrophic remodeling was induced on day 0 by subcutaneous implantation of an Ang II-containing osmotic minipump in the dorsal neck region. FI (50 mg/kg) was administered intraperitoneally every other day from one day prior to Ang II infusion through day 14.Total RNA was extracted from ventricular tissues (n=4 per group) at the endpoint using TRIzol reagent (Invitrogen) according to the manufacturer's protocol.

value: ventricular

value: WT

value: Ang II + FI


title: Ang II_FI_3

description: Library name: Sample 11


title: Ang II_FI_1

description: Library name: Sample 9


title: Ang II_FI_2

description: Library name: Sample 10


title: Ang II_4

description: Library name: Sample 8

value: Ang II + Vehicle


title: Ang II_1

description: Library name: Sample 5


title: Ang II_2

description: Library name: Sample 6


title: Ang II_3

description: Library name: Sample 7


title: Con_4

description: Library name: Sample 4

value: Saline + Vehicle


title: Con_3

description: Library name: Sample 3


title: Con_2

description: Library name: Sample 2


title: Con_1

description: Library name: Sample 1


title: Sham-3, Input

city: Guangzhou

first: Jingying

last: Liang

address: Jinsui Rd

institute: Zhongshan Ophthalmic Center

description: Library name: Sample12

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control.
Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads.
High quality reads were compared to the reference genome using HISAT2 (v2.0.4). And then HTSeq (v0.9.1) was used to obtain the original count number at gene level as mRNA expression profile.
edgeR (v3.16.5) was used to standardize and calculate the multiple change and p-value between the two groups of samples, and screen differentially expressed mRNA.
Different mRNA and lncRNA associated genes were analyzed by GO and KEGG.
Supplementary files format and content: CC_result(Mouse).xls
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx
Supplementary files format and content: mmu_pathwayResult.xls
Supplementary files format and content: MF_result(Mouse).xls
Supplementary files format and content: Differentially_methylated_sites.mRNA.xlsx
Supplementary files format and content: Differentially Expressed genes.xlsx
Supplementary files format and content: BP_result(Mouse).xls
Library strategy: MeRIP-seq

source_name: Retina

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA), and subjected to ribosomal RNA (rRNA) removal using GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China).
The rRNA- depleted samples were used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations. The RNA was fragmented into ~300 nt in length. The first-strand cDNA was synthesized from the RNA fragments by reverse transcriptase and random hexamer primers, and the second-strand cDNA was synthesized in 2nd Strand Synthesis Buffer with dUTP Mix. Then, the double stranded cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. The adapter-ligated DNA samples were PCR amplified and purified to obtain sequencing libraries. Finally, the libraries were sequenced with sequencer on the paired-end 150 bp mode.

value: Retina

value: Sham


title: Sham-2, Input

description: Library name: Sample11


title: RIR-3, Input

description: Library name: Sample9

value: RIR


title: Sham-1, Input

description: Library name: Sample10


title: RIR-2, Input

description: Library name: Sample8


title: RIR-1, Input

description: Library name: Sample7


title: Sham-2, IP

description: Library name: Sample5


title: Sham-3, IP

description: Library name: Sample6


title: RIR-2, IP

description: Library name: Sample2


title: RIR-1, IP

description: Library name: Sample1


title: RIR-3, IP

description: Library name: Sample3


title: BPN985, BPN/3J, vehicle, Kidney

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

description: Library name: LDL12001

data_processing:
Samples were processed using the nf-core/rnaseq v3.14.0 pipeline with nextflow v23.04.2.
Briefly, raw reads were trimmed using Trim Galore! v0.6.7 to remove low-quality bases and adapters. Trimmed reads were aligned to the human reference genome, mm39 with STAR v2.7.9a aligner
Finally, salmon Quant v1.10.1 is utilized for assigning reads.
Assembly: GCF_000001635.27_GRCm39_genomic
Supplementary files format and content: Tab delimited file with raw gene counts for every gene and every sample

source_name: kidney

extract_protocol:
Total RNA was extracted using the Aurum™ Total RNA Mini Kit (Bio-Rad Laboratories, Hercules, CA, USA). RNA concentration and purity were determined using NanoDrop One spectrophotometer UV–Vis (Bio-Rad Laboratories, USA). RNA samples (50 ng/µL) were reverse-transcribed into cDNA using the iScript cDNA Synthesis Kit on a T100™ Thermal Cycler (Bio-Rad, USA).
Total RNA was used to construct libraries using the VAHTS® Universal V8 RNAseq Library Prep Kit for Illumina NR605 and sequenced using Illumina NovaSeq6000 S4 flowcell PE150 sequencer at Azenta Life Sciences (Hangzhou, China).

treatment_protocol: Mice were treated with vehicle or Cmpd17b for 28 days once daily. Kidney tissues were collected for RNA sequencing.

value: kidney

tag: animal model

value: vehicle


title: BPN979, BPN/3J, Cmpd17b-treated Kidney

description: Library name: LDL12007


title: BPN999, BPN/3J, Cmpd17b-treated Kidney

description: Library name: LDL12008


title: BPN973, BPN/3J, vehicle, Kidney

description: Library name: LDL12000


title: BPN969, BPN/3J, vehicle, Kidney

description: Library name: LDL11999


title: I-epi-8w-Apc-2-749

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Assembly: The training method of the QIIME2 classifier follows these steps: - Extract all the read datafrom a reference database, in our report, SILVA version 138 with 99% similarity was used.
Supplementary files format and content: File name = abs-abund-table-7 (all 90 samples); Format = excel (.xlsx); Content = raw counts of sequencing reads for the bacteria strain
Supplementary files format and content: File name = rel-table-7 (all 90 samples); Format = excel (.xlsx); Content=relative abundance of sequencing reads for the bacteria strain

source_name: ileum epithelial cell

extract_protocol:
Fecalpellets werecollected asepticallyand placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit protocol.
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)
16S ribosomal RNA (rRNA) gene sequencing

value: ileum epithelial cell

value: ApcMin

value: Untreated

tag: time

value: 8 weeks old


title: BPN971, BPN/3J, Cmpd17b-treated Kidney

description: Library name: LDL12006


title: BPN967, BPN/3J, Cmpd17b-treated Kidney

description: Library name: LDL12005


title: BPN965, BPN/3J, Cmpd17b-treated Kidney

description: Library name: LDL12004


title: BPN1003, BPN/3J, vehicle, Kidney

description: Library name: LDL12003


title: BPH998, BPH/2J, vehicle, Kidney

description: Library name: LDL12013


title: BPH988, BPH/2J, vehicle, Kidney

description: Library name: LDL12012


title: BPH978, BPH/2J, Cmpd17b-treated Kidney

description: Library name: LDL12017


title: BPH990, BPH/2J, Cmpd17b-treated Kidney

description: Library name: LDL12018


title: BPH976, BPH/2J, Cmpd17b-treated Kidney

description: Library name: LDL12016


title: BPH962, BPH/2J, vehicle, Kidney

description: Library name: LDL12009


title: BPH966, BPH/2J, Cmpd17b-treated Kidney

description: Library name: LDL12014


title: BPH968, BPH/2J, Cmpd17b-treated Kidney

description: Library name: LDL12015


title: BPN983, BPN/3J, Cmpd17b-treated LV

description: Library name: LDH1674

source_name: Left ventricle

treatment_protocol: Mice were treated with vehicle or Cmpd17b for 28 days once daily. Left ventricle tissues were collected for RNA sequencing.

value: Left ventricle


title: BPH964, BPH/2J, vehicle, Kidney

description: Library name: LDL12010


title: BPN981, BPN/3J, vehicle, LV

description: Library name: LDH1672


title: BPN975, BPN/3J, vehicle, LV

description: Library name: LDH1668


title: BPN979, BPN/3J, Cmpd17b-treated LV

description: Library name: LDH1670


title: BPN973, BPN/3J, vehicle, LV

description: Library name: LDH1667


title: BPN967, BPN/3J, Cmpd17b-treated LV

description: Library name: LDH1661


title: BPN971, BPN/3J, Cmpd17b-treated LV

description: Library name: LDH1665


title: BPN965, BPN/3J, Cmpd17b-treated LV

description: Library name: LDH1659


title: BPN969, BPN/3J, vehicle, LV

description: Library name: LDH1663


title: BPN963, BPN/3J, vehicle, LV

description: Library name: LDH1657


title: BPN1003, BPN/3J, vehicle, LV

description: Library name: LDL12020


title: BPN1001, BPN/3J, vehicle, LV

description: Library name: LDL12019


title: BPH996, BPH/2J, Cmpd17b-treated LV

description: Library name: LDL12024


title: BPH988, BPH/2J, vehicle, LV

description: Library name: LDL12021


title: BPH982, BPH/2J, vehicle, LV

description: Library name: LDH1673


title: BPH980, BPH/2J, vehicle, LV

description: Library name: LDH1671


title: BPH984, BPH/2J, Cmpd17b-treated LV

description: Library name: LDH1675


title: BPH992, BPH/2J, Cmpd17b-treated LV

description: Library name: LDL12023


title: BPH978, BPH/2J, Cmpd17b-treated LV

description: Library name: LDH1669


title: BPH970, BPH/2J, vehicle, LV

description: Library name: LDH1664


title: BPH972, BPH/2J, Cmpd17b-treated LV

description: Library name: LDH1666


title: BPH968, BPH/2J, Cmpd17b-treated LV

description: Library name: LDH1662


title: BPH962, BPH/2J, vehicle, LV

description: Library name: LDH1656


title: BPH966, BPH/2J, Cmpd17b-treated LV

description: Library name: LDH1660


title: BPH964, BPH/2J, vehicle, LV

description: Library name: LDH1658


title: BPH1000, BPH/2J, vehicle, LV

description: Library name: LDL12022


title: I-epi-4w-Apc-5-741

value: 4 weeks old


title: PoH_rep1

description:
Library name: PoH1
Fecal sample from mouse treated with PO extract 3 g/kg via oral gavage daily for 3 days followed by APAP 300 mg/kg i.p., biological replicate 1

value: feces

value: PO extract 3 g/kg, p.o. daily for 3 days + APAP 300 mg/kg, i.p.


title: 64-sh-Acsf3_ZT21_REP4

city: Nantes

first: Daniel

last: Mauvoisin

address: 8 quai Moncousu

country: France

institute: Inserm

description: Library name: 64-sh-Acsf3_ZT21_REP4.fastq.gz

data_processing:
Raw reads were mapped using STAR on the GRCm38/mm10 genome assembly (Ensembl release 102). The BRB-seqTools suite (http://github.com/DeplanckeLab/BRB-seqTools) was subsequently applied to retrieve raw counts per gene.
Pipeline details have been published by Alpern et al. 2019 ( https://doi.org/10.1186/s13059-019-1671-x )
Assembly: GRCm38/mm10
Supplementary files format and content: Supplementary files format and content: tab-delimited umi count matrix

source_name: liver

extract_protocol:
RNA extraction was performed on frozen liver using Nucleozol following the manufacturer protocol (Macherey Nagel).
Pipeline details have been published by Alpern et al. 2019 ( https://doi.org/10.1186/s13059-019-1671-x )

value: liver

tag: zt

tag: replicate


title: I-epi-8w-WT-1-766


title: 63-sh-Acsf3_ZT18_REP4

description: Library name: 63-sh-Acsf3_ZT18_REP4.fastq.gz


title: 62-sh-Acsf3_ZT15_REP4

description: Library name: 62-sh-Acsf3_ZT15_REP4.fastq.gz


title: 61-sh-Acsf3_ZT12_REP4

description: Library name: 61-sh-Acsf3_ZT12_REP4.fastq.gz


title: 59-sh-Acsf3_ZT6_REP4

description: Library name: 59-sh-Acsf3_ZT6_REP4.fastq.gz


title: 60-sh-Acsf3_ZT9_REP4

description: Library name: 60-sh-Acsf3_ZT9_REP4.fastq.gz


title: 58-sh-Acsf3_ZT3_REP4

description: Library name: 58-sh-Acsf3_ZT3_REP4.fastq.gz


title: 57-sh-Acsf3_ZT0_REP4

description: Library name: 57-sh-Acsf3_ZT0_REP4.fastq.gz


title: 56-sh-Acsf3_ZT21_REP3

description: Library name: 56-sh-Acsf3_ZT21_REP3.fastq.gz


title: 55-sh-Acsf3_ZT18_REP3

description: Library name: 55-sh-Acsf3_ZT18_REP3.fastq.gz


title: 53-sh-Acsf3_ZT12_REP3

description: Library name: 53-sh-Acsf3_ZT12_REP3.fastq.gz


title: 54-sh-Acsf3_ZT15_REP3

description: Library name: 54-sh-Acsf3_ZT15_REP3.fastq.gz


title: 52-sh-Acsf3_ZT9_REP3

description: Library name: 52-sh-Acsf3_ZT9_REP3.fastq.gz


title: 51-sh-Acsf3_ZT6_REP3

description: Library name: 51-sh-Acsf3_ZT6_REP3.fastq.gz


title: 49-sh-Acsf3_ZT0_REP3

description: Library name: 49-sh-Acsf3_ZT0_REP3.fastq.gz


title: 48-sh-Acsf3_ZT21_REP2

description: Library name: 48-sh-Acsf3_ZT21_REP2.fastq.gz


title: 47-sh-Acsf3_ZT18_REP2

description: Library name: 47-sh-Acsf3_ZT18_REP2.fastq.gz


title: 45-sh-Acsf3_ZT12_REP2

description: Library name: 45-sh-Acsf3_ZT12_REP2.fastq.gz


title: 43-sh-Acsf3_ZT6_REP2

description: Library name: 43-sh-Acsf3_ZT6_REP2.fastq.gz


title: 41-sh-Acsf3_ZT0_REP2

description: Library name: 41-sh-Acsf3_ZT0_REP2.fastq.gz


title: 44-sh-Acsf3_ZT9_REP2

description: Library name: 44-sh-Acsf3_ZT9_REP2.fastq.gz


title: 46-sh-Acsf3_ZT15_REP2

description: Library name: 46-sh-Acsf3_ZT15_REP2.fastq.gz


title: 40-sh-Acsf3_ZT21_REP1

description: Library name: 40-sh-Acsf3_ZT21_REP1.fastq.gz


title: 38-sh-Acsf3_ZT15_REP1

description: Library name: 38-sh-Acsf3_ZT15_REP1.fastq.gz


title: 39-sh-Acsf3_ZT18_REP1

description: Library name: 39-sh-Acsf3_ZT18_REP1.fastq.gz


title: 36-sh-Acsf3_ZT9_REP1

description: Library name: 36-sh-Acsf3_ZT9_REP1.fastq.gz


title: 37-sh-Acsf3_ZT12_REP1

description: Library name: 37-sh-Acsf3_ZT12_REP1.fastq.gz


title: 35-sh-Acsf3_ZT6_REP1

description: Library name: 35-sh-Acsf3_ZT6_REP1.fastq.gz


title: 34-sh-Acsf3_ZT3_REP1

description: Library name: 34-sh-Acsf3_ZT3_REP1.fastq.gz


title: 33-sh-Acsf3_ZT0_REP1

description: Library name: 33-sh-Acsf3_ZT0_REP1.fastq.gz


title: 32-sh-Ctl_ZT21_REP4

description: Library name: 32-sh-Ctl_ZT21_REP4.fastq.gz

value: sh-Ctl


title: 31-sh-Ctl_ZT18_REP4

description: Library name: 31-sh-Ctl_ZT18_REP4.fastq.gz


title: 30-sh-Ctl_ZT15_REP4

description: Library name: 30-sh-Ctl_ZT15_REP4.fastq.gz


title: 29-sh-Ctl_ZT12_REP4

description: Library name: 29-sh-Ctl_ZT12_REP4.fastq.gz


title: 28-sh-Ctl_ZT9_REP4

description: Library name: 28-sh-Ctl_ZT9_REP4.fastq.gz


title: 27-sh-Ctl_ZT6_REP4

description: Library name: 27-sh-Ctl_ZT6_REP4.fastq.gz


title: 26-sh-Ctl_ZT3_REP4

description: Library name: 26-sh-Ctl_ZT3_REP4.fastq.gz


title: 24-sh-Ctl_ZT21_REP3

description: Library name: 24-sh-Ctl_ZT21_REP3.fastq.gz


title: 25-sh-Ctl_ZT0_REP4

description: Library name: 25-sh-Ctl_ZT0_REP4.fastq.gz


title: 20-sh-Ctl_ZT9_REP3

description: Library name: 20-sh-Ctl_ZT9_REP3.fastq.gz


title: 22-sh-Ctl_ZT15_REP3

description: Library name: 22-sh-Ctl_ZT15_REP3.fastq.gz


title: 21-sh-Ctl_ZT12_REP3

description: Library name: 21-sh-Ctl_ZT12_REP3.fastq.gz


title: 18-sh-Ctl_ZT3_REP3

description: Library name: 18-sh-Ctl_ZT3_REP3.fastq.gz


title: 19-sh-Ctl_ZT6_REP3

description: Library name: 19-sh-Ctl_ZT6_REP3.fastq.gz


title: 17-sh-Ctl_ZT0_REP3

description: Library name: 17-sh-Ctl_ZT0_REP3.fastq.gz


title: 16-sh-Ctl_ZT21_REP2

description: Library name: 16-sh-Ctl_ZT21_REP2.fastq.gz


title: 15-sh-Ctl_ZT18_REP2

description: Library name: 15-sh-Ctl_ZT18_REP2.fastq.gz


title: 14-sh-Ctl_ZT15_REP2

description: Library name: 14-sh-Ctl_ZT15_REP2.fastq.gz


title: Glioma_RNA_SCIENCE_2

first: Evgeny

last: Deforzh

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

institute: Brigham and Women's Hospital

description: Library name: Sample 4

data_processing:
Duplicate reads were collapsed into a fasta file, with duplicate counts per read calculated using fastx_toolkit (version 0.0.14).
Chimeric reads were aligned to a reference fasta file containing transcript sequences (hg38_Homo_sapiens.GRCh38.100.fasta) using BWA-MEM in local alignment mode considered transcript strand only
Pairs of genes from each chimeric read were identified, and the number of reads for each gene pair was quantified with ChiRA
Assembly: GRCh38/hg38

source_name: primary glioma tumors

extract_protocol:
Nuclei were distributed into 96-well plates by limiting dilution. Nuclear membranes were lysed and chromatin was reverse-crosslinked by incubation with Proteinase K for 4 h at 65 °C followed by 15 min 95 °C to deactivate Proteinase K.  Biotinylated RNA complexes were captured using streptavidin magnetic beads and transferred to fresh wells. For 3′ RNA end repair, bead-enriched RNA–RNA crosslinked material was washed in ice-cold T4 polynucleotide kinase (PNK) buffer and treated with 0.5 U T4 PNK (NEB) in an 80-µL reaction at 37 °C for 4 h. Subsequently, fresh ATP (1 mM final) and an additional 0.5 U T4 PNK were added in a total volume of 100 µL and incubated for 1 h at 37 °C to repair 5′ RNA ends, followed by the removal of the buffer. RNA–RNA chimeras were generated by ligation in T4 RNA ligase buffer (NEB) supplemented with 1 mM ATP, 0.5 U/µL RNase inhibitor, and 2.5 U/µL T4 RNA ligase 1 (NEB) at 37 °C for 1 h with continuous agitation. Reverse crosslinking was completed by UV irradiation at 254 nm for 5 min on ice. RNA on Streptavidine beads was washed once with 1x scRT Buffer (Takara, #634444).
RT and subsequent steps were performed using the SMART-Seq® Stranded Kit (Takara, #634444), following the manufacturer’s instructions.

value: primary glioma tumors

value: WT


title: 13-sh-Ctl_ZT12_REP2

description: Library name: 13-sh-Ctl_ZT12_REP2.fastq.gz


title: 12-sh-Ctl_ZT9_REP2

description: Library name: 12-sh-Ctl_ZT9_REP2.fastq.gz


title: 11-sh-Ctl_ZT6_REP2

description: Library name: 11-sh-Ctl_ZT6_REP2.fastq.gz


title: 10-sh-Ctl_ZT3_REP2

description: Library name: 10-sh-Ctl_ZT3_REP2.fastq.gz


title: 9-sh-Ctl_ZT0_REP2

description: Library name: 9-sh-Ctl_ZT0_REP2.fastq.gz


title: 8-sh-Ctl_ZT21_REP1

description: Library name: 8-sh-Ctl_ZT21_REP1.fastq.gz


title: 7-sh-Ctl_ZT18_REP1

description: Library name: 7-sh-Ctl_ZT18_REP1.fastq.gz


title: 6-sh-Ctl_ZT15_REP1

description: Library name: 6-sh-Ctl_ZT15_REP1.fastq.gz


title: 5-sh-Ctl_ZT12_REP1

description: Library name: 5-sh-Ctl_ZT12_REP1.fastq.gz


title: 4-sh-Ctl_ZT9_REP1

description: Library name: 4-sh-Ctl_ZT9_REP1.fastq.gz


title: 3-sh-Ctl_ZT6_REP1

description: Library name: 3-sh-Ctl_ZT6_REP1.fastq.gz


title: 2-sh-Ctl_ZT3_REP1

description: Library name: 2-sh-Ctl_ZT3_REP1.fastq.gz


title: 1-sh-Ctl_ZT0_REP1

description: Library name: 1-sh-Ctl_ZT0_REP1.fastq.gz


title: GBM TAM, Pracinostat, biological replicate 4

city: Stanford

first: Mona

last: Khalaj

state: California

address: 265 Campus Drive

institute: Stanford University

description:
Library name: Pracinostat4
Column name in gene_symbol_counts.tsv: Pracinostat4

data_processing:
Technical replicate FASTQ files from two sequencing lanes were merged prior to processing.
Adapter trimming and quality filtering were performed using Trim Galore!, and read quality was assessed using FastQC. Reads were aligned to the mouse reference genome (GRCm39, GENCODE release M37) using STAR, and gene-level quantification was performed using RSEM.
nf-core/rnaseq pipeline v3.20.0 was used with default parameters. Quality control was assessed using FastQC, RSeQC, Qualimap, and MultiQC.
Gene-level expected counts were filtered to remove mitochondrial and rRNA genes and genes with zero counts across all samples. Differential gene expression analysis was performed using DESeq2 on raw gene counts, with Wald tests and Benjamini-Hochberg correction used to calculate statistical significance.
Assembly: GRCm39 (GENCODE release M37)
Supplementary files format and content: Tab-delimited text file (gene_symbol_counts.tsv) containing RSEM rounded expected counts per gene (rows) per sample (columns), filtered to remove mitochondrial/rRNA genes and zero-count genes.

source_name: brain tumor, orthotopic xenograft

growth_protocol: NSG mice bearing orthotopic T387 GBM xenografts were treated with Pracinostat (30 mg/kg, oral gavage) or DMSO vehicle control four times per week for three weeks beginning 7 days after tumor implantation.

extract_protocol:
At study endpoint, tumors were dissociated and CD11b+ tumor-associated macrophages were FACS sorted. Total RNA was extracted from sorted CD11b+ cells using the miRNeasy Micro Kit (Qiagen) with QIAzol lysis reagent.
Libraries were prepared using the Takara Bio SMARTer Stranded Total RNA-Seq Kit v3 (Cat. #634485) with 1 ng of total RNA input. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 with a NovaSeq SP flow cell (300-cycle, 2x150 bp paired-end reads) across two lanes per sample.

treatment_protocol: Pracinostat was prepared in 10% DMSO, 40% PEG300, 5% Tween-80, 45% PBS at 3 mg/kg final concentration and administered orally. Vehicle-treated mice received the same solvent mixture without drug.

value: brain tumor, orthotopic xenograft

value: CD11b+ tumor-associated macrophages

value: Pracinostat 30 mg/kg oral 4x/week 3 weeks


title: GBM TAM, Pracinostat, biological replicate 1

description:
Library name: Pracinostat1
Column name in gene_symbol_counts.tsv: Pracinostat1


title: GBM TAM, Pracinostat, biological replicate 2

description:
Library name: Pracinostat2
Column name in gene_symbol_counts.tsv: Pracinostat2


title: GBM TAM, Pracinostat, biological replicate 3

description:
Library name: Pracinostat3
Column name in gene_symbol_counts.tsv: Pracinostat3


title: GBM TAM, DMSO vehicle, biological replicate 3

description:
Library name: DMSO3
Column name in gene_symbol_counts.tsv: DMSO3

value: DMSO vehicle


title: GBM TAM, DMSO vehicle, biological replicate 2

description:
Library name: DMSO2
Column name in gene_symbol_counts.tsv: DMSO2


title: GBM TAM, DMSO vehicle, biological replicate 1

description:
Library name: DMSO1
Column name in gene_symbol_counts.tsv: DMSO1