title: 16S amplicon sequencing of sample GHIA_Faeces_7

description:
Library name: GHIA_Faeces_7
16S V3-V4 amplicon sequencing


title: HIFRAP_1_1

status: Public on Feb 12 2026

type: SRA

city: Oxford

first: Vinay

last: Shukla

state: United Kingdom

address: South Parks Road Oxford

department: Department of Biology

country: India

institute: University of Oxford

description: Library name: Sample 4

library_source: transcriptomic

data_processing:
Kallisto read allignment, edgeR differenital expression
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: gene_fpkm.txt

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Whole seedling

extract_protocol:
RNA was isolated using GeneJET RNA Purification Kit (Thermo Scientific™) as per manufacturer’s instruction.
cDNA library preparation were carried out as described in Dalle Carbonare L., 2025

tag: tissue

value: Whole seedling

tag: genotype

tag: treatment

value: Hypoxia


title: Patient 1, baseline and end-of-treatment (HTO data)

city: New York

first: Juan-Jose

last: Garces

state: NY

address: 1275 York Ave

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Library name: SD-2589_1-HTO

library_source: other

data_processing:
Matrices with filtered unique molecular identifier (UMI) counts and peaks from cellranger ARC outputs were used as input for Seurat. Furthermore, these were filtered out according to the following criteria: (i) more than 5,000 or less than 500 expressed genes, (ii) more than 20,000 or less than 500 peak counts, (iii) a TSS (transcription start site) enrichment >1, (iv) a nucleosome signal <2, and (v) a percentage of mitochondrial genes ≥25%. Antibody-hashed cells were then demultiplexed taking the union of both Seurat’s HTODemux and the R package scDemultiplex. For more stringent criteria, expression-based doublets were additionally removed using the package R scds. All samples were merged into the same object in the final step.
Assembly: GRCh38
Supplementary files format and content: Filtered count and barcode matrices as Cellranger outputs
Supplementary files format and content: HTO information for sample demultiplexing
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
Viably frozen paired bone marrow mononuclear cells from baseline and W52 from 13 participants (1001, 1003, 1004, 1006, 1009, 1011, 1012, 1013, 1014, 1015, 1017, 1022 and 1023) were sorted by fluorescence-activated cell sorting (FACS) for live CD45+ single cells (CD45: BD Bioscience, catalog# 563204; DAPI: Millipore Sigma, catalog# 508741) and submitted for single-cell sequencing in 0.04% bovine serum albumin in PBS.
They were processed using the Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280). We followed the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide with the difference that single-cell suspension was prepared as described (DOGMA-seq protocol with Digitonin buffer). Briefly, cells were treated with a digitonin lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.01% digitonin and 2 U/µl of RNase inhibitor) for 5 min on ice, followed by adding 1 mL of chilled wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, and 1 U/µl of RNAse inhibitor) and inversion before centrifugation at 500g for 5 min at 4 °C. The supernatant was discarded, and cells were resuspended in digitonin wash buffer, followed by counting using trypan blue and DAPI on a Countess II FL Automated Cell Counter. In addition, samples for each patient were pooled together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO). Final libraries were sequenced on an Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

treatment_protocol: High-fiber plan-based diet

value: Bone marrow

tag: cell line

value: Immune microenvironment

tag: cell type

value: CD45+ sorted cells


title: 16S amplicon sequencing of sample GHIA_Faeces_6

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
Library name: GHIA_Faeces_6
16S V3-V4 amplicon sequencing

library_source: genomic

data_processing:
from raw to demultiplexed fastq files please contact BMR Sequencing Services (Padova, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNBGCWSCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores $threads --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 249 --p-trunc-len-r 150 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
qiime feature-classifier classify-consensus-vsearch --i-query clean_rep-seqs.qza --i-reference-reads $silva_ref --i-reference-taxonomy $silva_tax --p-perc-identity 0.99 --p-threads $threads --o-classification taxonomy_vsearch.qza --o-search-results vsearch_hits.qza --verbose 2> ASV_matched_in_SILVA.txt
qiime metadata tabulate --m-input-file taxonomy_SILVA.qza --o-visualization confidence_taxonomy_SILVA.qzv
Assembly: SILVA 138
Supplementary files format and content: dna-sequences.fasta: sequences of representative ASVs
Supplementary files format and content: feature_table.tsv: ASV abundance table
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Faeces

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Faeces

value: Bacteria consortium

value: Control


title: 16S amplicon sequencing of sample GHIA_Faeces_5

description:
Library name: GHIA_Faeces_5
16S V3-V4 amplicon sequencing


title: Patient 13, baseline and end-of-treatment (HTO data)

description: Library name: SD-2589_13-HTO


title: HIFRAP_0_4

description: Library name: Sample 3


title: Patients 1015 and 1012, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2520_1015_1012_BL_ES-GEX

library_source: transcriptomic single cell

data_processing:
Matrices with filtered unique molecular identifier (UMI) counts and peaks from cellranger ARC outputs were used as input for Seurat. Furthermore, these were filtered out according to the following criteria: (i) more than 5,000 or less than 500 expressed genes, (ii) more than 20,000 or less than 500 peak counts, (iii) a TSS (transcription start site) enrichment >1, (iv) a nucleosome signal <2, and (v) a percentage of mitochondrial genes ≥25%. Antibody-hashed cells were then demultiplexed taking the union of both Seurat’s HTODemux and the R package scDemultiplex. For more stringent criteria, expression-based doublets were additionally removed using the package R scds. All samples were merged into the same object in the final step.
Assembly: GRCh38
Supplementary files format and content: Filtered count and barcode matrices as Cellranger outputs
Supplementary files format and content: HTO information for sample demultiplexing

molecule: polyA RNA


title: Severe_MalariaSample_HepaticDysfunction_2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression Profiling

hyb_protocol: Labeled cRNA samples were fragmented at 60°C and hybridized onto an Agilent Custom Plasmodium vivax Gene Expression Microarray 8X60K using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method .

organism: Plasmodium vivax

source_name: Total RNA, Test Group 1, Sample 2

label_protocol: Samples were labeled using an Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA was reverse transcribed at 40°C using an oligo dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA was used as the template for cRNA generation. cRNA was generated by in vitro transcription, and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

extract_protocol:
Clinical samples collected from malaria patients
RNA from enriched blood was isolated using TRIzol as per manufacture's protocols.

treatment_protocol: Total RNA was extracted from venous blood samples collected from malaria patients. The patients exhibited symptoms categorized as un-complicated (n =5), hepatic dysfunction (n=9).

value: Enriched blood sample

tag: clinical complication

value: Severe malaria - Hepatic Dysfunction


title: Severe_MalariaSample_HepaticDysfunction_1

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 1


title: Patients 1015 and 1012, baseline and end-of-treatment (HTO data)

description: Library name: SD-2520_1015_1012_BL_ES-HTO


title: Uncomplicated_MalariaSample_3

description: Gene expression Profiling

source_name: Total RNA, Control Sample 3

value: Uncomplicated Malaria


title: Uncomplicated_MalariaSample_5

description: Gene expression Profiling

source_name: Total RNA, Control Sample 5


title: HIFRAP_0_3

description: Library name: Sample 2


title: 16S amplicon sequencing of sample GHIA_Faeces_4

description:
Library name: GHIA_Faeces_4
16S V3-V4 amplicon sequencing


title: 16S amplicon sequencing of sample GHIA_Faeces_3

description:
Library name: GHIA_Faeces_3
16S V3-V4 amplicon sequencing


title: Uncomplicated_MalariaSample_2

description: Gene expression Profiling

source_name: Total RNA, Control Sample 2


title: Patient 1004, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2520_1004_BL_ES-GEX


title: 16S amplicon sequencing of sample GHIA_Faeces_2

description:
Library name: GHIA_Faeces_2
16S V3-V4 amplicon sequencing


title: CUT&Tag IgG control library of Irx3-overexpressing AC16 cells (OE)

city: Changchun

first: BIng

last: Li

address: 130021, No. 1, Xinmin Street, Chaoyang District, Changchun, Jilin Province

country: China

institute: First Hospital of Jilin University

description:
Library name: OE-IRX3-igg-lib1
Library was sequenced on a SURFSeq 5000 instrument; the instrument model field in the metadata reflects the closest available option (FASTASeq 300) in the provided dropdown list.

data_processing:
Raw data was quality-controlled with FastQC and trimmed by Cutadapt (v2.5) to remove adapters and low-quality reads, generating clean data.
Clean reads were mapped to the reference genome (human: GRCh38/hg38) using Bowtie2 (v2.3.5.1). Unique mapped paired reads were extracted and sorted via SAMtools (v1.9), with PCR duplicates removed.
Significant peaks were identified by MACS2 (v2.2.6); bigWig files for visualization were generated using deepTools (v3.4.1).
Assembly: GRCh38/hg38 (UCSC)
Supplementary files format and content: OE-1-IRX3_peaks.narrowPeak: BED format, records significant binding peaks of Irx3 in OE-1 sample
Supplementary files format and content: OE-1-IRX3_summits.bed: BED format, records peak summit positions of Irx3 in OE-1 sample
Supplementary files format and content: OE-2-IRX3_peaks.narrowPeak: BED format, records significant binding peaks of Irx3 in OE-2 sample
Supplementary files format and content: OE-2-IRX3_summits.bed: BED format, records peak summit positions of Irx3 in OE-2 sample

source_name: Cardiomyocytes

growth_protocol: Human AC16 cardiomyocytes: Cultured in DMEM/F-12 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO₂ and saturated humidity.

extract_protocol:
CUT&Tag was performed via the Epi™ CUT&Tag Kit (Cat. No. R1823, Epibiotek, China). Briefly, 5 × 10⁴ to 1.5 × 10⁵ cells were washed with PBS and incubated with activated ConA magnetic beads. The cells were sequentially incubated with primary and secondary antibodies, followed by washing steps. The pAG-Tn5 transposase was diluted 1:100 and incubated with the sample for 1 hour at room temperature. The reaction was initiated by adding reaction buffer containing MgCl₂ and incubated at 37 °C for 1 hour. The reaction was stopped with 10% SDS and incubated at 55 °C for 10 minutes. DNA was purified via 1.8× Epi™ DNA Clean Beads (Cat. No. R1809).
CUT&Tag libraries were prepared using 2× AmpliMix with N5/N7 index primers. The PCR conditions were as follows: 98 °C for 30 s; 14 cycles of 98 °C for 15 s, 60 °C for 20 s, and 72 °C for 8 s; and a final extension at 72 °C for 2 min. Amplified libraries were purified and analyzed for fragment size distribution via the Bioptic Qsep100 system, followed by sequencing and downstream data analysis.

treatment_protocol: AC16 cells were infected with Irx3-overexpressing lentivirus (MOI=10, HanBio) with 5 μg/mL polybrene

value: Cardiomyocytes

value: Cardiomyocyte


title: HIFRAP_0_2

description: Library name: Sample 1


title: mRNA Q901 24h rep3

city: Nam-gu, Pohang-si

first: Hyerim

last: Jung

state: Gyeongsangbuk-do

address: 47, Jigok-ro

department: Dept. of Life Sciences

country: South Korea

institute: Pohang University of Science & Technology (POSTECH)

description: Library name: MCF7-24hr-QS1409-3

data_processing:
mRNA-seq data were trimmed with Trim Galore and aligned to hg38 (v36) using STAR (2.7.8a_2021-03-08)[47]. The bigWig files were generated by deepTools bamCoverage and visualized with UCSC genome browser. The expression level was calculated with RSEM rsem-calculate-expression (v1.3.1)[48] and DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: MCF-7 was maintained in DMEM (Thermo Fisher Scientific, Waltham, MA, USA, Gibco™, 31053028) with 10% FBS (Invitrogen, Carlsbad, CA, USA, 10091148), GlutaMAX (Thermo Fisher Scientific, Gibco™, 35050061) and Penicillin-Streptomycin (Welgene, Gyeongsansi, South Korea, LS202-02) ), and for short-term treatment, DMEM (Gibco™, 31053028) with 10% charcoal stripped FBS (Gibco™, A3382101), and GlutaMAX (Gibco™, 35050061) was used.

extract_protocol:
For mRNA-seq, Total RNA was prepared from MCF-7 cells after Q901 treatment using TRIzol (Invitrogen, 15596026) according to the manufacturer’s protocol.
mRNA-seq library was constructed using the MGIEasy RNA Directional Library Prep Kit (MGI, Shenzhen, China) according to the manufacturer’s instructions.

treatment_protocol: For the short-term condition, MCF-7 cells were treated with DMSO or 100 nM Q901 for 1 h followed by 1 h of EtOH/E2 treatment (the E2 condition was not used in this study). For long-term treatment, MCF-7 cells were treated with DMSO or 100 nM Q901 for 4, 24 h.


title: Patient 1004, baseline and end-of-treatment (HTO data)

description: Library name: SD-2520_1004_BL_ES-HTO


title: Patient 1003, baseline and end-of-treatment (HTO data)

description: Library name: SD-2520_1003_BL_ES-HTO


title: mRNA DMSO 24h rep3

description: Library name: MCF7-24hr-DMSO-3

value: DMSO 24h


title: CUT&Tag library of Irx3-overexpressing AC16 cells (OE-1)

description:
Library name: OE-1-IRX3-lib1
Library was sequenced on a SURFSeq 5000 instrument; the instrument model field in the metadata reflects the closest available option (FASTASeq 300) in the provided dropdown list.


title: Patient 1003, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2520_1003_BL_ES-GEX


title: CUT&Tag library of Irx3-overexpressing AC16 cells (OE-2)

description:
Library name: OE-2-IRX3-lib1
Library was sequenced on a SURFSeq 5000 instrument; the instrument model field in the metadata reflects the closest available option (FASTASeq 300) in the provided dropdown list.


title: Uncomplicated_MalariaSample_4

description: Gene expression Profiling

source_name: Total RNA, Control Sample 4


title: First tarsal segment, male, 12h APF, scRNA-seq

city: Davis

first: Ben

last: Hopkins

state: CA

address: One Shields Avenue

department: Evolution & Ecology

institute: UC Davis

description:
Library name: DMEL12HM
Chromium Next GEM Single Cell 3’ kit v3.1

data_processing:
The reference index was built using the ‘mkref’ function in CellRanger (v7.0.0) and the Ensembl BDGP6.32 Drosophila melanogaster genome into which we introduced sequences for GAL4, GFP, and mCherry. The GTF was filtered to include features of gene_biotype ‘ncRNA’ and ‘protein_coding’.  Alignment, barcode assignment, and UMI counting were performed on each single-cell dataset using the ‘count’ function in CellRanger. For each dataset, we ran ‘count’ with default settings (including counting regions that mapped to intronic regions), other than using the ‘force-cells’ option to limit the number of cells detected to 12,000 (except in the case of the 24h female dataset where we used 14,000).
Assembly: Ensembl BDGP6.32 Drosophila melanogaster genome
Supplementary files format and content: All processed datasets uploaded are the components of the filtered feature barcode matrix output from cell ranger.

organism: Drosophila melanogaster

source_name: First tarsal segment

extract_protocol:
We prepared our single-cell suspensions from dissected first tarsal segment tissue following the protocol we previously developed as part of our cell atlas (Hopkins et al., 2023 PLOS Biology) and which is available on protocols.io (dx.doi.org/10.17504/protocols.io.x54v9dzbmg3e/v2). Briefly, white prepupae were collected, sexed, and transferred to folded kimwipe wet with water (300μl for 12h, 450μl for 20h, and 750μl for 36h) held inside a petri dish. The dish was moved to an incubator at 25°C on a 12:12 cycle and the pupae left to age. Pupae were removed from puparia using forceps and placed on top of a water-soaked kimwipe 1 h before the desired age was reached (e.g., 23 h after collection for the 24 h sample). Pupae were then placed ventral side up on tape, the base of the abdomen pierced to release fluid pressure, and the foreleg removed at the tibia/tarsal joint. The dissected leg was moved to a piece of tape, covered in a drop of 1X Dulbecco’s PBS (DPBS, Sigma, D8537), and a Micro Knife (Fine Science Tools, 10318–14) used to sever at the midpoint of the second tarsal segment. The first tarsal segment was then eased out of the pupal cuticle and transferred to a glass well on ice containing 100μl of 1X DPBS using a BSA-coated 10μl tip. Once 65-70 segments were collected, the DPBS was removed from the well and replaced with 100μl of dissociation buffer, which consisted of 10X TrypLE (Thermo Fisher Scientific, A12177-01) with a final concentration of 2 mg/mL of collagenase (Sigma, C0130). The well was sealed and submerged in a metal bead bath in an incubator at 37°C for 35 minutes. For the 36h APF sample, we incubated for 45 minutes to overcome the greater resistance to dissociation at this point. The dissociation buffer was then removed from the well and replaced with 50μl of room temperature DPBS before the suspension was pipetted up and down 20-40x using a 200μl, widebore, low bind, freshly BSA coated tip (Thermo Fisher Scientific, 2069G) on a 50μl pipette set to 40μl. The solution was then pipetted up and down a further 20-40x using a flame-rounded, BSA-coated 200μl tip, again on a 50μl pipette set to 40μl. Next, the solution was transferred to a 2mL, low-bind, wide-bottomed tube on ice. Cell concentration and viability was assayed using an acridine orange/propidium iodide stain and measured using a LUNA-FL Fluorescent Cell Counter averaged across 2 × 5μl aliquots.
Barcoded 3’ single cell libraries were prepared from single cell suspensions using the Chromium Next GEM Single Cell 3’ kit v3.1(10X Genomics, Pleasanton, California) for sequencing according to the manufacturer’s instructions.  The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. Libraries from the 16h, 20h, 24h, 30h, and 36h APF samples were sequenced on a NovaSeq 6000 sequencer (Illumina, San Diego, CA) with paired-end 150 bp reads. The 12h APF libraries were sequenced in a 28 x 10 x 10 x 90 bp configuration on an AVITI sequencer (Element Biosciences, San Diego, CA).  In each case, the sequencing generated approximately 50,000 reads per cell and 500 million reads per library .

value: First tarsal segment

tag: Sex

value: Male

tag: age

value: 12h APF

value: dsx-GAL4 > UAS-mCherry


title: mRNA Q901 4h, rep3

description: Library name: MCF7-4hr-QS1409-3


title: 16S amplicon sequencing of sample GHIA_Faeces_17

description:
Library name: GHIA_Faeces_17
16S V3-V4 amplicon sequencing

value: Shocked


title: Uncomplicated_MalariaSample_1

description: Gene expression Profiling

source_name: Total RNA, Control Sample 1


title: 16S amplicon sequencing of sample GHIA_Faeces_16

description:
Library name: GHIA_Faeces_16
16S V3-V4 amplicon sequencing


title: 16S amplicon sequencing of sample GHIA_Faeces_18

description:
Library name: GHIA_Faeces_18
16S V3-V4 amplicon sequencing


title: First tarsal segment, female, 12h APF, scRNA-seq

description:
Library name: DMEL12HF
Chromium Next GEM Single Cell 3’ kit v3.1

value: Female


title: humanCAR-T_ponatinib_1

city: Tsukiji

first: Yuki

last: Okuhiro

state: Tokyo-to

country: Japan

institute: National cancer center research institute

description:
Library name: sample3
10x Genomics

data_processing:
Raw base call files were demultiplexed into FASTQ format using the "cellranger mkfastq" pipeline. Read filtering, alignment to the human reference genome (hg38), and generation of gene-barcode matrices were performed using Cell Ranger "count" (10x Genomics) with default parameters.
Assembly: human reference genome (hg38)
Supplementary files format and content: Processed data include a gene-cell count matrix (matrix.mtx), cell barcodes (barcodes.tsv), gene annotations (features.tsv), and cell metadata (metadata.tsv). Format follows the standard 10x Genomics output structure.

source_name: human CAR-T cells

extract_protocol:
CAR-T cells were washed, re-suspended in FACS buffer and stained with a Viability Dye, CD4, CD8, EGFR. Cells were sorted using a FACS Discover (BD Biosciences) into CD4+ CAR-T cells (CD4+ EGFR+ cells) and CD8+ CAR-T cells (CD8+ EGFR+ cells). Cells were washed and re-suspended in RPMI-1640 supplemented with 10% FBS.  Finally, samples were prepared by mixing CD4+ CAR-T cells and CD8+ CAR-T cells at a 1:9 ratio.
Single-cell suspensions were prepared and processed using the 10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 according to the manufacturer’s instructions. Approximately [insert number] cells per sample were loaded into the Chromium Controller to generate gel bead-in-emulsions (GEMs) for cell and molecular barcoding. Following reverse transcription and cDNA amplification, sequencing libraries were constructed following the standard 10x Genomics protocol. Library quality was assessed using an Agilent Bioanalyzer with a High Sensitivity DNA Kit.

treatment_protocol: CD3+ T cells purified from PBMCs of healthy individuals were activated with anti-CD3 and CD28 monoclonal antibodies and lentivirally transduced with the anti-CD19-BBz CAR gene with DMSO or ponatinib (100 nM) in RPMI-1640 supplemented with 10% Fetal bovine serum (FBS) and 4 mM L-glutamine (Thermo Fisher Scientific; Cat. #25030-081). Recombinant human IL-7 (R&D System, #207-IL) and IL-15 (R&D System, #247-ILB) were added at 10 ng/mL. Beads were removed on day 4 using a magnet, and cells were rested for a further 4 days.

value: human CAR-T cells

value: paired-end

value: ponatinib


title: 16S amplicon sequencing of sample GHIA_Faeces_14

description:
Library name: GHIA_Faeces_14
16S V3-V4 amplicon sequencing

value: Faeces

value: Bacteria consortium


title: 16S amplicon sequencing of sample GHIA_Faeces_13

description:
Library name: GHIA_Faeces_13
16S V3-V4 amplicon sequencing


title: mRNA Q901 4h, rep2

description: Library name: MCF7-4hr-QS1409-2


title: mRNA Q901 24h rep2

description: Library name: MCF7-24hr-QS1409-2


title: 16S amplicon sequencing of sample GHIA_Faeces_15

description:
Library name: GHIA_Faeces_15
16S V3-V4 amplicon sequencing


title: mRNA DMSO 24h rep2

description: Library name: MCF7-24hr-DMSO-2


title: Lib3-viral-library-prep3-rep1

city: Seattle

first: Lukas

last: Oesinghaus

state: WA

address: 3946 W Stevens Wy NE

institute: University of Washington

description:
Library name: Lib3-viral-library-prep3-rep1
immune cell: viral transduction

data_processing:
The UMI was extracted and added to the read name using custom python scripts. Libraries were aligned to the reference sequences using BWA-MEM. Alignments were filtered using a custom python script. UMIs were deduplicated using a custom script with unique matching. Alignments for each reference were counted using a custom python script. Further downstream processing was performed using custom python scripts.
Supplementary files format and content: Processed data is provided as .csv files. They contain: Raw counts, log2FC, and normalized stability data for plasmid stability assays. Raw counts and calculated half-life values for Actinomycin D data. Raw counts, calculated relative distribution across polysome peaks and mean ribosome load for polysome profiling data. Metadata necessary for the analysis of the actionmycin D and polysome profiling data.

molecule: other

organism: synthetic construct

source_name: CD8 T cell

extract_protocol:
Protocol 1 and 2: If cells were adherent, they were detached cells with TrypLE. Cells were spun down for 5 min at 210 g. We resuspended the cells in 1 ml of cold PBS and placed them on ice. We took 25 µl of each sample, added 175 µl of PBS, and measured the GFP fluorescence on the Attune NxT flow cytometer to determine cell numbers and transfection efficiencies. We used the Monarch Total RNA Miniprep Kit (NEB, T2010S) to purify total RNA. We eluted in 100 µl of nuclease-free water and determined concentrations using a NanoDrop 2000c (Thermo Fisher). mRNA was purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L). We eluted in 18 µl of nuclease-free water. mRNA was reverse transcribed and amplified using custom primers. Protocol 3: Cells were pelleted (100 g RT, then 1000 g 4°C after PBS wash) and frozen at −80°C. The appropriate spike-in amount was calibrated using a t=0 sample by testing serial spike-in dilutions and estimating relative spike-in vs. cellular RNA abundance via qPCR. The selected spike-in amount (targeting the highest spike-in species at ~2x the most abundant cellular mRNA at t=0) was added to all samples during lysis (NEB RNA miniprep kit), followed by library preparation and sequencing as described above. Protocol 4: Cells were treated with cycloheximide and lysed. Media was replaced with 5 mL RT DPBS + CHX, incubated 5 min at 37°C, replaced with ice-cold DPBS + CHX, and cells were lysed in 300 µL cold lysis buffer. Lysates were incubated on ice (10 min), homogenized (25G needle), centrifuged (16,000 g, 5 min, 4°C), treated with DNase I (0.005 U/µL, 30 min, ice), and stored at -80°C. Polysome profiling was performed using 20–55% sucrose gradients (100 mM KCl, 20 mM HEPES pH 7.2, 10 mM MgCl₂) prepared by overnight diffusion at 4°C. Lysates were layered onto gradients and ultracentrifuged (151,000 g, 3 h, SW-41 Ti rotor). ~25 fractions were collected; free RNA and visible polysome peak fractions were retained for downstream analysis. Spike-in calibration was performed on total lysate by testing serial spike-in dilutions followed by Trizol extraction and RNA purification (Zymo RNA C&C-5 kit). qPCR curves were used to determine the spike-in amount targeting the most abundant spike-in species at ~2x the most abundant endogenous mRNA in the average fraction. All fractions were then processed with spike-in addition, Trizol extraction (scaled volumes), column purification, and standard library preparation. Fractions corresponding to the same polysome peak were combined during purification. mRNA isolation (magnetic beads) was performed for total lysate and free ribosome fractions only; ribosome-bound fractions were assumed to be mRNA-enriched.
Custom workflow

value: CD8 T cell


title: mRNA DMSO 4h rep2

description: Library name: MCF7-4hr-DMSO-2

value: DMSO 4h


title: 16S amplicon sequencing of sample GHIA_Faeces_12

description:
Library name: GHIA_Faeces_12
16S V3-V4 amplicon sequencing


title: humanCAR-T_ponatinib_2

description:
Library name: sample4
10x Genomics


title: humanCAR-T_DMSO_2

description:
Library name: sample2
10x Genomics

value: DMSO


title: mRNA DMSO 4h rep3

description: Library name: MCF7-4hr-DMSO-3


title: Lib3-viral-library-prep2-rep2

description:
Library name: Lib3-viral-library-prep2-rep2
immune cell: viral transduction


title: humanCAR-T_DMSO_1

description:
Library name: sample1
10x Genomics


title: Lib3-viral-library-prep3-rep2

description:
Library name: Lib3-viral-library-prep3-rep2
immune cell: viral transduction


title: Lib3-viral-library-prep2-rep1

description:
Library name: Lib3-viral-library-prep2-rep1
immune cell: viral transduction


title: THP-1_OE_ZBTB7A_Rep3

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

description:
Library name: BL-15
THP1oe-ZBTB7A_day10_rep3_S6
Z7AOE_counts.normalized.xlsx
dge.Z7AOE-vs-Ctrl.q005.xlsx

data_processing:
Reads were mapped to the transcriptome annotations assembly with RSEM v1.2.4, modified to utilize Bowtiw v1.0.0 with the '-v 2' option
Reminaing unaligned reads were mapped to the genome and a database of possible splice junctions with TopHat v2.0.8b. The resulting alignments generated by TopHat were combined with the RSEM outputs. Reads that spanned splice junctions had to have at least a 6nt overhang.
Assembly: hg38
Supplementary files format and content: Processed Data contains normalized counts for each sample
Supplementary files format and content: Processed Data contains differential expression analysis

growth_protocol: THP-1 cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS), 1% Penicillin/Streptomycin, and 1% GlutaMAX in a humidified incubator at 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted with the Rneasy Plus Mini Kit (Qiagen) and QIAshredder following the manufacturer's protocol.
Poly(A) mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module using ~1µg of total RNA as input following the manufacturer's protocol. The NEXTflex Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) was used to generate cDNA libraries utilizing the NEXTflex RNA-Seq barcodes accoridng to the manufacturer's protocol. Libraries were sequenced using a Nova-Seq X with 150bp paired end reads.

treatment_protocol: All sgRNA sequences were annealed and phosphorylated and cloned into the LRG2.1 vector.All cDNA constructs were cloned into a lentiviral vector (EF1α-IRES-Puromycin-T2A-ZsGreen). Spin infections for all constructs were performed at 32ºC at 1500 RCF (xg) for 90min with 5µg/mL polybrene and lentiviral supernatants. Cells were collected 3 or 6 days after transduction and processed for RNA isolation and library preparations.

value: Acute Myeloid Leukemia

value: ZBTB7A OE

value: Lentiviral infection and overexpression


title: mRNA Q901 24h rep1

description: Library name: MCF7-24hr-QS1409-1


title: THP-1_OE_ZBTB7A_Rep2

description:
Library name: BL-14
THP1oe-ZBTB7A_day10_rep2_S5
Z7AOE_counts.normalized.xlsx
dge.Z7AOE-vs-Ctrl.q005.xlsx


title: Lib3-viral-library-prep1-rep2

description:
Library name: Lib3-viral-library-prep1-rep2
immune cell: viral transduction


title: 16S amplicon sequencing of sample GHIA_Faeces_11

description:
Library name: GHIA_Faeces_11
16S V3-V4 amplicon sequencing


title: 16S amplicon sequencing of sample GHIA_Faeces_10

description:
Library name: GHIA_Faeces_10
16S V3-V4 amplicon sequencing

value: Control


title: THP-1_OE_ZBTB7A_Rep1

description:
Library name: BL-13
THP1oe-ZBTB7A_day10_rep1_S4
Z7AOE_counts.normalized.xlsx
dge.Z7AOE-vs-Ctrl.q005.xlsx


title: mRNA DMSO 24h rep1

description: Library name: MCF7-24hr-DMSO-1

value: DMSO 24h


title: THP-1_OE_Ctrl_Rep3

description:
Library name: BL-12
THP1oe-Ctrl_day10_rep3_S3
Z7AOE_counts.normalized.xlsx
dge.Z7AOE-vs-Ctrl.q005.xlsx


title: 16S amplicon sequencing of sample GHIA_Faeces_1

description:
Library name: GHIA_Faeces_1
16S V3-V4 amplicon sequencing


title: mRNA Q901 4h, rep1

description: Library name: MCF7-4hr-QS1409-1


title: Lib3-viral-library-prep1-rep1

description:
Library name: Lib3-viral-library-prep1-rep1
immune cell: viral transduction


title: Lib3-plasmid-library-rep2

description:
Library name: Lib3-plasmid-library-rep2
immune cell: viral transduction


title: 16S amplicon sequencing of sample GHIA_Colon_9

description:
Library name: GHIA_Colon_9
16S V3-V4 amplicon sequencing

source_name: Colon

value: Colon


title: mRNA DMSO 4h rep1

description: Library name: MCF7-4hr-DMSO-1


title: THP-1_OE_Ctrl_Rep2

description:
Library name: BL-11
THP1oe-Ctrl_day10_rep2_S2
Z7AOE_counts.normalized.xlsx
dge.Z7AOE-vs-Ctrl.q005.xlsx


title: mRNA Q901 1h, EtOH 1h rep2

description: Library name: QS1409-1h-EtOH-1h-rep2

value: Q901 1h, EtOH 1h


title: Lib3-plasmid-library-rep1

description:
Library name: Lib3-plasmid-library-rep1
immune cell: viral transduction


title: 16S amplicon sequencing of sample GHIA_Colon_7

description:
Library name: GHIA_Colon_7
16S V3-V4 amplicon sequencing


title: Lib3-P2C2-MSCV-rep2

description:
Library name: Lib3-P2C2-MSCV-rep2
immune cell: viral transduction


title: mRNA DMSO 1h, EtOH 1h rep2

description: Library name: DMSO-1h-EtOH-1h-rep2

value: DMSO 1h, EtOH 1h


title: THP-1_OE_Ctrl_Rep1

description:
Library name: BL-10
THP1oe-Ctrl_day10_rep1_S1
Z7AOE_counts.normalized.xlsx
dge.Z7AOE-vs-Ctrl.q005.xlsx


title: THP-1_sgZBTB7A_g23_Rep3

description:
Library name: BL-9
Sample23_S151_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx

value: ZBTB7A KO

value: Lentiviral infection and knockout


title: 16S amplicon sequencing of sample GHIA_Colon_8

description:
Library name: GHIA_Colon_8
16S V3-V4 amplicon sequencing


title: Lib3-P2C2-MSCV-rep1

description:
Library name: Lib3-P2C2-MSCV-rep1
immune cell: viral transduction


title: Lib3-NIH3T3-plasmid-rep2

description:
Library name: Lib3-NIH3T3-plasmid-rep2
immune cell: viral transduction


title: 16S amplicon sequencing of sample GHIA_Colon_6

description:
Library name: GHIA_Colon_6
16S V3-V4 amplicon sequencing


title: mRNA Q901 1h, EtOH 1h rep1

description: Library name: QS1409-1h-EtOH-1h-rep1


title: 16S amplicon sequencing of sample GHIA_Colon_5

description:
Library name: GHIA_Colon_5
16S V3-V4 amplicon sequencing


title: THP-1_sgZBTB7A_g23_Rep2

description:
Library name: BL-8
Sample23_b_S157_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: THP-1_sgZBTB7A_g23_Rep1

description:
Library name: BL-7
Sample23_a_S154_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: Lib3-NIH3T3-plasmid-rep1

description:
Library name: Lib3-NIH3T3-plasmid-rep1
immune cell: viral transduction


title: mRNA DMSO 1h, EtOH 1h rep1

description: Library name: DMSO-1h-EtOH-1h-rep1


title: Late treatment mouse liver tumor (LT03), single-cell RNA-seq

city: Suita

first: Shuhei

last: Yamamoto

state: Osaka

address: 2-2 Yamadaoka, Suita, Osaka

institute: Osaka University, Graduate School of Medicine

description:
Library name: LT03_scRNAseq
Liver tumor from late treatment mouse (LT), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ

data_processing:
Raw sequencing reads were processed using the Seven Bridges platform. Reads were aligned to the mouse reference genome (Mus musculus GRCm38, mm10), and gene expression counts were generated for each cell using GENCODE M19 annotation (gencode.vM19.annotation.gtf).
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: Single-cell gene expression matrix (genes × cells). Each file corresponds to one sample.

organism: Mus musculus

source_name: liver

extract_protocol:
Liver tumors were excised from mice, mechanically dissociated, and single-cell suspensions were enriched for immune cells using CD45 MicroBeads prior to library preparation.
Single-cell libraries were prepared from dissociated liver tumor cells using the BD Rhapsody Whole Transcriptome Analysis (WTA) protocol, following the manufacturer’s instructions.

value: liver


title: 16S amplicon sequencing of sample GHIA_Colon_3

description:
Library name: GHIA_Colon_3
16S V3-V4 amplicon sequencing


title: THP-1_sgZBTB7A_g21_Rep2

description:
Library name: BL-5
Sample21_b_S156_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: Lib3-HEK293T-plasmid-rep2

description:
Library name: Lib3-HEK293T-plasmid-rep2
immune cell: viral transduction


title: THP-1_sgZBTB7A_g21_Rep1

description:
Library name: BL-4
Sample21_a_S153_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: Lib3-HEK293T-plasmid-rep1

description:
Library name: Lib3-HEK293T-plasmid-rep1
immune cell: viral transduction


title: Late treatment mouse liver tumor (LT01), single-cell RNA-seq

description:
Library name: LT01_scRNAseq
Liver tumor from late treatment mouse (LT), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ


title: 16S amplicon sequencing of sample GHIA_Colon_2

description:
Library name: GHIA_Colon_2
16S V3-V4 amplicon sequencing


title: Late treatment mouse liver tumor (LT02), single-cell RNA-seq

description:
Library name: LT02_scRNAseq
Liver tumor from late treatment mouse (LT), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ


title: Lib3-gDNA-P2C2-rep1

description:
Library name: Lib3-gDNA-P2C2-rep1
immune cell: viral transduction


title: Early treatment mouse liver tumor (ST03), single-cell RNA-seq

description:
Library name: ST03_scRNAseq
Liver tumor from early treatment mouse (ST), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ


title: Lib3-gDNA-P2C2-rep2

description:
Library name: Lib3-gDNA-P2C2-rep2
immune cell: viral transduction


title: THP-1_sgRosa_Rep3

description:
Library name: BL-3
Rosa_S149_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx

value: WT


title: 16S amplicon sequencing of sample GHIA_Colon_18

description:
Library name: GHIA_Colon_18
16S V3-V4 amplicon sequencing

value: Shocked


title: 16S amplicon sequencing of sample GHIA_Colon_17

description:
Library name: GHIA_Colon_17
16S V3-V4 amplicon sequencing

value: Bacteria consortium


title: THP-1_sgZBTB7A_g21_Rep3

description:
Library name: BL-6
Sample21_S150_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: Lib3-gDNA-CD8T-E2-rep2

description:
Library name: Lib3-gDNA-CD8T-E2-rep2
immune cell: viral transduction

value: CD8 T cell


title: Early treatment mouse liver tumor (ST02), single-cell RNA-seq

description:
Library name: ST02_scRNAseq
Liver tumor from early treatment mouse (ST), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ


title: 16S amplicon sequencing of sample GHIA_Colon_16

description:
Library name: GHIA_Colon_16
16S V3-V4 amplicon sequencing


title: 16S amplicon sequencing of sample GHIA_Colon_4

description:
Library name: GHIA_Colon_4
16S V3-V4 amplicon sequencing


title: Early treatment mouse liver tumor (ST01), single-cell RNA-seq

description:
Library name: ST01_scRNAseq
Liver tumor from early treatment mouse (ST), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ


title: Lib3-gDNA-CD8T-E2-rep1

description:
Library name: Lib3-gDNA-CD8T-E2-rep1
immune cell: viral transduction


title: THP-1_sgRosa_Rep1

description:
Library name: BL-1
Rosa_a_S152_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: THP-1_sgRosa_Rep2

description:
Library name: BL-2
Rosa_b_S155_L004
Z7AKO_counts.normalized.xlsx
dge.Z7AKO-vs-WT.q005.xlsx


title: 16S amplicon sequencing of sample GHIA_Colon_15

description:
Library name: GHIA_Colon_15
16S V3-V4 amplicon sequencing


title: Lib3-gDNA-CD8T-E1-rep2

description:
Library name: Lib3-gDNA-CD8T-E1-rep2
immune cell: viral transduction


title: Vehicle-treated mouse liver tumor (Control03), single-cell RNA-seq

description:
Library name: Control03_scRNAseq
Liver tumor from vehicle-treated mouse (Control), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ.


title: Arp8_mut_20min_BiolRep2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: Library name: L24

data_processing:
Reads were aligned to genome and transcripts abundance was estimated using Kallisto (v. 0.48)
Assembly: Saccharomyces_cerevisiae.R64-1-1.108
Supplementary files format and content: Kallisto output files with pseudocounts and TPM values

organism: Saccharomyces cerevisiae

growth_protocol: ARP8 wild-type and arp-8-P strains were  grown overnight to OD 600nm = 0.8 - 1.0 in 10 ml YPD complete media. Next day, cells were reinoculated in 100ml fresh YPAD media at 0.1 OD. At OD 600 nm = 0.4 cells were collected.

extract_protocol:
Total RNA was Trizol/chloroform-extracted, precipitated using isopropanol and resuspended in water. Before library preparation, RNA was treated with DNase I and purified using RNAClean XP beads.
1 µg DNaseI-treated RNA was subjected to rRNA depletion using the S. cerevisiae - specific riboPOOL kit (siTOOLs Biotech) according to the manufacturers protocol. Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers protocol.

treatment_protocol: See the accompanying paper for details of alpha factor arrest.

value: MAT a, his3delta1 leu2delta0 ura3delta0 ARP8::ARP8-S65A, S233A

value: alpha factor arrest and release into S phase


title: 16S amplicon sequencing of sample GHIA_Colon_14

description:
Library name: GHIA_Colon_14
16S V3-V4 amplicon sequencing


title: Arp8_mut_10min_BiolRep2

description: Library name: L23


title: Vehicle-treated mouse liver tumor (Control02), single-cell RNA-seq

description:
Library name: Control02_scRNAseq
Liver tumor from vehicle-treated mouse (Control), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ.


title: Lib3-CD8T-rested-E2-rep2

description:
Library name: Lib3-CD8T-rested-E2-rep2
immune cell: viral transduction


title: Treated with DMXAA in KO BMMs_3

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

description:
Library name: KO_DMXAA_III
Thailand

data_processing:
Sequencing was carried out on a DNBseq (2 × 150 bp paired end reads).
RNA-Seq  reads were aligned to the Mus musculus reference genome mm10.
Reads were mapped and aligned using Hisat2 and quantified with the R package Rsubread (featureCounts)
Assembly: mm10
Supplementary files format and content: Differentially expressed genes

source_name: Bone morrow-derived macrophage

growth_protocol: Bone marrow-derived macrophages (BMMs) from wild-type (WT) and MGMT Knockout (KO) mice

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, USA) The quality and concentrations of RNA were measured by a NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific).
RNA libraries were prepared using a DNBSEQ Eukaryotic Strand-specific mRNA library kit (BGI Genomics, Shenzhen, China).

treatment_protocol: Macrophages were treated with either DMSO (vehicle control) or DMXAA for 24 hours.

value: Bone morrow-derived macrophage

value: MGMT KO

value: DMXAA

tag: batch


title: Vehicle-treated mouse liver tumor (Control01), single-cell RNA-seq

description:
Library name: Control01_scRNAseq
Liver tumor from vehicle-treated mouse (Control), dissociated into single cells and analyzed by BD Rhapsody WTA, sequenced on DNBSEQ.


title: Arp8_WT_20min_BiolRep2

description: Library name: L21

value: MAT a, his3delta1 leu2delta0 met15delta0 ura3delta0


title: Arp8_mut_20min_BiolRep1

description: Library name: L18


title: 16S amplicon sequencing of sample GHIA_Colon_13

description:
Library name: GHIA_Colon_13
16S V3-V4 amplicon sequencing


title: Treated with DMXAA in KO BMMs_2

description:
Library name: KO_DMXAA_II
Thailand


title: 16S amplicon sequencing of sample GHIA_Colon_12

description:
Library name: GHIA_Colon_12
16S V3-V4 amplicon sequencing


title: Lib3-gDNA-CD8T-E1-rep1

description:
Library name: Lib3-gDNA-CD8T-E1-rep1
immune cell: viral transduction


title: 16S amplicon sequencing of sample GHIA_Colon_10

description:
Library name: GHIA_Colon_10
16S V3-V4 amplicon sequencing

value: Control


title: Lib3-CD8T-rested-E2-rep1

description:
Library name: Lib3-CD8T-rested-E2-rep1
immune cell: viral transduction


title: Treated with DMXAA in KO BMMs_1

description:
Library name: KO_DMXAA_I
Thailand


title: Arp8_mut_10min_BiolRep1

description: Library name: L17


title: 16S amplicon sequencing of sample GHIA_Colon_11

description:
Library name: GHIA_Colon_11
16S V3-V4 amplicon sequencing

value: Colon


title: Lib3-CD8T-rested-E1-rep2

description:
Library name: Lib3-CD8T-rested-E1-rep2
immune cell: viral transduction


title: 16S amplicon sequencing of sample GHIA_Colon_1

description:
Library name: GHIA_Colon_1
16S V3-V4 amplicon sequencing


title: Arp8_WT_10min_BiolRep2

description: Library name: L20


title: Lib3-CD8T-rested-E1-rep1

description:
Library name: Lib3-CD8T-rested-E1-rep1
immune cell: viral transduction


title: Treated with DMSO in KO BMMs_2

description:
Library name: KO_DMSO_III
Thailand

value: DMSO


title: Arp8_WT_10min_BiolRep1

description: Library name: L14


title: Arp8_WT_20min_BiolRep1

description: Library name: L15


title: Treated with DMSO in KO BMMs_3

description:
Library name: KO_DMSO_IV
Thailand


title: WT_ATAC-seq_NGO_rep1

first: Satoshi

middle: H

last: Namekawa

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

description: Library name: WT_ATAC-seq_NGO_rep1

data_processing:
Raw paired-end ATAC-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to either the mouse (GRCm38/mm10) genomes using bowtie2 (version 2.3.3.1) with default arguments.
The aligned reads were filtered to remove alignments mapped to multiple locations by calling grep with the -v option before being subjected to downstream analyses.
PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute).
Biological replicates were pooled for visualization and other analyses after validation of reproducibility.
Peak calling for ATAC-seq data was performed using MACS3 (version 3.0.0a7) with default arguments.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: primary cells

extract_protocol:
FACS-sorted cells were isolated from ovaries and pooled as one replicate. Samples were lysed in 50 μl of lysis buffer (10 mM Tris–HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) on ice for 10 min. Immediately after lysis, nuclei were spun at 500 × g for 10 min at 4 °C to remove the supernatant.
Nuclei were then incubated 10 μl of transposition mix (0.5 µl homemade Tn5 transposase, 5 µl 2× TD buffer (10 mM Tris–HCl (pH 7.6), 10 mM MgCl2, and 20% Dimethyl Formamide), 3.3 µl PBS, 0.1 μl 1% digitonin, 0.1 μl 10% Tween-20, and 1 μl water) at 37 °C for 30 min in a thermomixer with shaking at 500 rpm.
the transposed DNA was purified with a MinElute kit (Qiagen). DNA libraries were prepared through the omni-ATAC method (PMID: 28846090)

value: ovary

value: P5-6 non-growing oocytes


title: Arp8_mut_BiolRep3

value: MAT a, his3{delta}1 leu2{delta}0 ura3{delta}0 ARP8::ARP8-S65A, S233A


title: Lib3-CD8T-lateactivated-E2-rep1

description:
Library name: Lib3-CD8T-lateactivated-E2-rep1
immune cell: viral transduction


title: WT_ATAC-seq_NGO_rep2

description: Library name: WT_ATAC-seq_NGO_rep2


title: Lib3-CD8T-lateactivated-E2-rep2

description:
Library name: Lib3-CD8T-lateactivated-E2-rep2
immune cell: viral transduction


title: WT_ATAC-seq_P1O_rep1

description: Library name: WT_ATAC-seq_P1O_rep1

value: P1 oocytes


title: Treated with DMXAA in WT BMMs_3

description:
Library name: WT_DMXAA_III
Thailand

value: Wild-type (WTfl/fl)


title: WT_ATAC-seq_P1O_rep2

description: Library name: WT_ATAC-seq_P1O_rep2

value: WT


title: Lib3-CD8T-exhausted-E2-rep2

description:
Library name: Lib3-CD8T-exhausted-E2-rep2
immune cell: viral transduction


title: Treated with DMSO in KO BMMs_1

description:
Library name: KO_DMSO_II
Thailand


title: Treated with DMXAA in WT BMMs_2

description:
Library name: WT_DMXAA_II
Thailand


title: Lib3-CD8T-exhausted-E2-rep1

description:
Library name: Lib3-CD8T-exhausted-E2-rep1
immune cell: viral transduction


title: Lib3-CD8T-exhausted-E1-rep2

description:
Library name: Lib3-CD8T-exhausted-E1-rep2
immune cell: viral transduction


title: Arp8_WT_BiolRep2

value: MAT a, his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Arp8_mut_BiolRep2


title: WT_ATAC-seq_E18O_rep1

description: Library name: WT_ATAC-seq_E18O_rep1

value: E18.5 oocytes


title: WT_ATAC-seq_E18O_rep2

description: Library name: WT_ATAC-seq_E18O_rep2


title: Treated with DMXAA in WT BMMs_1

description:
Library name: WT_DMXAA_I
Thailand


title: Lib3-CD8T-earlyactivated-E2-rep2

description:
Library name: Lib3-CD8T-earlyactivated-E2-rep2
immune cell: viral transduction

value: CD8 T cell


title: Arp8_mut_BiolRep1


title: Lib3-CD8T-exhausted-E1-rep1

description:
Library name: Lib3-CD8T-exhausted-E1-rep1
immune cell: viral transduction


title: Arp8_WT_BiolRep3


title: Treated with DMSO in WT BMMs_3

description:
Library name: WT_DMSO_IV
Thailand


title: Treated with DMSO in WT BMMs_2

description:
Library name: WT_DMSO_III
Thailand


title: 20181217_1of2

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

description: Library name: 20181217_1of2

data_processing:
fastq files were demultiplexed using droptag.
demultiplexed fastq files were processed with the project yaml file provided as supplementary file and using the indrops pipeline https://github.com/indrops/indrops
reads were filtered remove low quality reads
filtered reads were indexed and sorted by barcode of origin
reads from every barcode were aligned using Bowtie, and quantified to produce UMIFM counts
Assembly: GRCz11
Supplementary files format and content: gzipped text file of gene counts

organism: Danio rerio

source_name: tumor in adrenal gland

growth_protocol: All zebrafish used in this study were derived from the AB background strain (ZIRC Cat# ZL1, RRID: ZIRC_ZL1), and embryos/juvenile fish were staged according to Kimmel et al (PMID: 8589427). Transgenic zebrafish lines MYCN and MYCN;LMO1 were generated and validated by sorting and genotyping as described in our previous publications (PMID: 22439933, PMID: 28867147). Both lines were heterozygous and randomly assigned to experimental groups.

extract_protocol:
Single-cell whole transcriptome amplification was performed using the Fluidigm C1 Single-Cell Auto Prep System (C1 System) as per the manufacturer’s recommendations (full details available at Fluidigm.com). Briefly, tumor was collected and dissociated with collagenase. The cell suspension was filtered through 35um nylon mesh and resuspended at a concentration of 250 cell per μL of complete media, mixed 7:3 with C1 suspension reagent (Fluidigm), and loaded onto C1 Single-Cell Auto Prep chips (C1 chips; Fluidigm). After loading, each of the cell isolation chambers on the C1 chip was optically inspected for the presence of a cell.
Single cells was lysed and SMART-Seq (Ramskold et al., 2012) whole transcriptome amplified products were prepared with the C1 System using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) and protocols provided by Fluidigm. The whole transcriptome amplification products were harvested from the C1 chip, diluted to a concentration of 0.15 ng/μL, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per the manufacturer’s recommendations.

value: tumor in adrenal gland

value: mycnonly


title: Treated with DMSO in WT BMMs_1

description:
Library name: WT_DMSO_II
Thailand

value: Bone morrow-derived macrophage


title: Mouse iTN NKX22 ChIP rep2

status: Public on Feb 11 2026

first: Sumin

last: Jang

institute: Columbia University

description: Library name: iTN_NKX22_rep2

data_processing:
Aligned to reference genome via STAR
Assembly: mm10, hg38
Supplementary files format and content: read count (tab-delimited text)

source_name: spinal motor neuron organoid

extract_protocol:
Qiagen FFPE Rneasy for human, Qiagen Rneasy for mouse
Illumina Truseq PolyA library prep

value: spinal motor neuron organoid

value: pMN+Nkx22 expression

value: DOX


title: 20181217_2of2

description: Library name: 20181217_2of2


title: Mouse iTN NKX22 ChIP rep1

description: Library name: iTN_NKX22_rep1


title: Lib3-CD8T-earlyactivated-E2-rep1

description:
Library name: Lib3-CD8T-earlyactivated-E2-rep1
immune cell: viral transduction


title: Mouse iTN H3K27ac ChIP rep1

description: Library name: iTN_H3K27ac_rep1


title: Mouse iWT NKX22 ChIP rep2

description: Library name: iWT_NKX22_rep2


title: Mouse noDOX H3K27ac ChIP rep2

description: Library name: noDOX_H3K27ac_rep2

value: pMN


title: Arp8_WT_BiolRep1


title: Mouse iWT H3K27ac ChIP rep2

description: Library name: iWT_H3K27ac_rep2


title: Mouse iWT H3K27ac ChIP rep1

description: Library name: iWT_H3K27ac_rep1


title: Mouse iWT NKX22 ChIP rep1

description: Library name: iWT_NKX22_rep1


title: Mouse_iNkx22TNmut_rep3

description: Library name: iTN_rep3


title: Mouse noDOX H3K27ac ChIP rep1

description: Library name: noDOX_H3K27ac_rep1


title: Mouse_iNkx22WT_rep2

description: Library name: iWT_rep2


title: Mouse_iNkx22TNmut_rep1

description: Library name: iTN_rep1


title: Mouse_iNkx22SDmut_rep3

description: Library name: iSD_rep3


title: Mouse_iNkx22WT_rep1

description: Library name: iWT_rep1


title: Mouse_noDOX_rep3

description: Library name: noDOX_rep3

value: no DOX


title: Mouse_iNkx22SDmut_rep1

description: Library name: iSD_rep1


title: Mouse iTN H3K27ac ChIP rep2

description: Library name: iTN_H3K27ac_rep2


title: Mouse_iNkx22WT_rep3

description: Library name: iWT_rep3


title: Mouse_iNkx22TNmut_rep2

description: Library name: iTN_rep2


title: H4K16ac-KAT8-cKO-R848

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
Genome mapping was performed using Bowtie (version:0.12.8) and clean reads were compared to reference genome mm10. MACS (version 2.2.7.1) was applied to call peak.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameter was set as fold change ≥ 2 or≤ 1/2 and P value < 0.05, and the differences between the obtained peakswere annotated.
The annotation program was the same as the above peak annotation program, including different peak location information, annotation information, etc.
Assembly: mm10
Supplementary files format and content: narrowPeak file
Library strategy: CUT&Tag

source_name: Mus musculus

growth_protocol: BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml).

extract_protocol:
CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions. Briefly, WT and KAT8-deficient BMDMs were stimulated with R848 for 2h, and then harvested after PBS wash. Cells (1 × 105) were bound with concanavalin A-coated magnetic beads and then incubated with antibodies against H4K16ac (CST) at 4 °C overnight. On the next day, samples were incubated with a second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted.
The librarys were constructed by purified DNA, and amplified using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions.

treatment_protocol: WT and KAT8-deficient BMDMs were stimulated with R848(100ng/ml) for 2h

value: Mus musculus

value: bone marrow

value: Mouse primary bone marrow-derived macrophages


title: BMDM,R848

description: ATAC-seq

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Fastx v0.0.13, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.2.6. Only uniquely mapping reads with at most two mismatches were retained.
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were renormalized (to reads per million, rpkm) and reformatted in the narrowPeak file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.05
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: Bone marrow

extract_protocol:
Cells were trypsinized with 0.25% trypsin-EDTA and resuspended in 1X PBS (calcium and magnesium-free).
For the ATAC-seq library preparation, 5×104 viable cells were used and collected. The cell pellets were resuspended in cold lysis buffer (1 M Tris-HCl, pH 7.4, 5 M NaCl, 1 M MgCl2, IGEPALCA-630) and incubated on ice for 5 min. Then, the cells were collected and resuspended with 50 μl transposition mixtures according to ATAC Kit instructions (Vazyme, #TD501). Mixtures were incubated for the PCR reaction. Mixtures were purified with VAHTS DNA Clean Beads (Vazyme, #N411) and amplified for 15 cycles using TruePrep Index Kit V2 for Illumina (Vazyme #TD202). Amplification products were further purified with VAHTS DNA Clean Beads.
Mixtures were incubated for the PCR reaction. Mixtures were purified with VAHTS DNA Clean Beads (Vazyme, #N411) and amplified for 15 cycles using TruePrep Index Kit V2 for Illumina (Vazyme #TD202).

treatment_protocol: BMDMs were stimulated with R848 (100ng/ml) for 0h and 2h

value: Bone marrow

value: BMDM

value: Bone marrow-derived macrophages


title: BMDM,KAT8,UT

extract_protocol:
CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions. Briefly, BMDMs were stimulated with R848 for 0h and 2h, and then harvested after PBS wash. Cells (1 × 105) were bound with concanavalin A-coated magnetic beads and then incubated with antibodies against KAT8 (ProteinTech) at 4 °C overnight. On the next day, samples were incubated with a second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted.
The librarys were constructed by purified DNA, and amplified using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions.

treatment_protocol: BMDMs were stimulated with R848(100ng/ml) for 2h or not.

value: untreated


title: BMDM,UT

description: ATAC-seq

value: WT


title: genomic_DNA_from_control_placenta_7

type: genomic

city: Szczecin

first: Magdalena

last: Bednarek-Jedrzejek

address: Rybacka 1

country: Poland

institute: Pomeranian Medical University in Szczecin

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data were processed in R, normalized using BMIQ normalization
Normalized beta-value (BMIQ)

label: Cy3 and Cy5

source_name: Placenta

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the samples was extracted using standard salting out method

value: Placenta


title: genomic_DNA_from_FGR_placenta_11


title: genomic_DNA_from_FGR_placenta_10


title: Mouse_noDOX_rep1

description: Library name: noDOX_rep1


title: BMDM,KAT8,R848


title: Mouse_noDOX_rep2

description: Library name: noDOX_rep2


title: genomic_DNA_from_FGR_placenta_8


title: H4K16ac-WT-R848


title: genomic_DNA_from_control_placenta_5


title: genomic_DNA_from_FGR_placenta_6


title: genomic_DNA_from_FGR_placenta_9


title: genomic_DNA_from_control_placenta_6


title: genomic_DNA_from_FGR_placenta_7


title: genomic_DNA_from_FGR_placenta_5


title: genomic_DNA_from_FGR_placenta_4


title: genomic_DNA_from_FGR_placenta_2


title: genomic_DNA_from_FGR_placenta_1


title: genomic_DNA_from_control_placenta_4


title: KOLF, WT-1

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

description: Library name: Run80_52_CF132_KOLF_WT_4_9

data_processing:
Amplicon sequencing: reads were aligned to either WT or VUS amplicon using CRISPResso2
Assembly: VUS and WT amplicon
Supplementary files format and content: All processed files show all reads and alignments to the reference and genetic variant amplicons

source_name: KOLF

growth_protocol: KOLF2-C1 (KOLF2) cells were grown in 6-well plates coated with Matrigel® hESC-Qualified Matrix, LDEV-free (Corning®) maintained in TeSR-E8 media (STEMCELL Technologies), and media changed daily. Cells were split with Gentle Cell Dissociation Reagent (STEMCELL Technologies) (16). Cell cryopreservation was in KnockOut™ Serum Replacement medium (Gibco™) supplemented with 10% DMSO. All cultures were maintained at 37°C humidified 5% CO2 incubator, unless otherwise stated, and were routinely tested for mycoplasma. Both variant and control KOLF2 iPSCs, were differentiated using the STEMdiff Ventricular or Atrial Cardiomyocyte Differentiation Kits (STEMCELL, Australia) and subsequently maintained in the corresponding Maintenance Kit.

extract_protocol:
Next-generation amplicon sequencing was carried out on the MiniSeq Sequencing System (Illumina©). In brief, a 250bp GATA4_HDR site PCR product was amplified, from gDNA, with GATA4 pAMPF1 (5’ACACTCTTTCCCTACACGACGCTCTTCCGATCTcaccttttacttggacatgaagc3’) and GATA4 pAMPR1 (5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgtacaaaggaagaagacaaggga3’) (21) for 150bp, paired end, >10,000 reads (MiniSeq, Illumina, Australia) and reads aligned to the HDR or WT amplicon with CRISPResso2 software (22)
RNA libraries were prepared with the SureSelect Strand-Specific XT HS2 Poly-A kit and sequenced at Genomics WA (Perth, Australia) on an Illumina NovaSeq 6000 platform (paired-end, 100bp. ~30 million reads per sample).

value: KOLF

value: induced pluripotent stem cell


title: genomic_DNA_from_control_placenta_1


title: ChIP-seq analysis of MYRFL genomic target locations in HEK293, THC0616TANN_MYRFL_ChIP2

city: Toronto

first: Arttu

last: Jolma

state: Ontario

address: 160 College Street, Room 1350

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: Library name: THC0616GPZN_MYRFL_ChIP2

data_processing:
Constant flank derived bases were removed with Cutadapt (using the adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Reads were mapped into human genome build hg38 with bowtie2 (options: --very-sensitive, --no-unal). The mapped trimmed reads were filtered using samtools (options: -q 30, -F 1548, version 1.20)
Peak calling was performed with MACS2 using sample-specific backgrounds [made by merging pull-down experiments; PMID: 27852650].
Assembly: hg38
Supplementary files format and content: Bigwig files are based on Bowtie2 mapping followed by MACS3 peak calling.
Supplementary files format and content: Narrowpeak files have been derived following the custom Peak calling was performed with MACS2 using sample-specific backgrounds [made by merging pull-down experiments; PMID: 27852650].

growth_protocol: HEK293 cells were grown and maintained in high glucose DMEM supplemented with 10% FBS. TF cell lines were established via transfection and selection of transfected cells in 200ug/ml of hygromycin in growth media.

extract_protocol:
20 million cells were cross-linked with 1% formaldehyde and palletted in cold PBS. Cell pallettes were lysed in a 3 step lysis procedure and chromatin was sonicated at the last step. Sonicated chromatin ws immunoprecipitated using anti-eGFP IgG (Rabbit polycclonal, abcam290) coated magnetic beads. For "input" control samples, 10ul of pre-IP sample were collected. After de-cross linking and DNA purification, both ChIP and Input samples were eluted in 60ul of elution buffer.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit and protocol

treatment_protocol: Established TF cell lines were treated with 1ug/ml of doxycycline 24 hours prior to cross linking. The TF expressions were confirmed using fluorescent microscopy and observation of GFP.

tag: hngc symbol_of_the_analyzed_protein

value: MYRFL

tag: sample type

value: ChIP

value: Approved


title: Pre-IP control THC0746TANN_MYRFL_INPUT1

description: Library name: THC0746GPZN_MYRFL_INPUT1

value: Input

value: No expert curation due to insufficient peak numbers


title: ChIP-seq analysis of TTF1 genomic target locations in HEK293, THC0808TANN_TTF1_ChIP2

description: Library name: THC0808GPZN_TTF1_ChIP2


title: KOLF, WT-2

description: Library name: Run80_54_CF132_KOLF_WT_6


title: ChIP-seq analysis of ZNF518B genomic target locations in HEK293, THC0477TANN_ZNF518B_ChIP2

description: Library name: THC0477GPZN_ZNF518B_ChIP2


title: KOLF, VUS-2

description: Library name: Run80_53_CF132_KOLF_GATA4VUS2_2

value: VUS


title: genomic_DNA_from_FGR_placenta_3


title: Pre-IP control THC0436TAND_TIGD5_INPUT1

description: Library name: THC0436GPZD_TIGD5_INPUT1


title: ChIP-seq analysis of KDM5B genomic target locations in HEK293, THC0402TANM_KDM5B_ChIP1

description: Library name: THC0402GPZM_KDM5B_ChIP1

value: Not approved


title: KOLF, VUS-1

description: Library name: Run80_51_CF132_KOLF_GATA4VUS2_4_5


title: ChIP-seq analysis of CGGBP1 genomic target locations in HEK293, THC0539TANN_CGGBP1_ChIP1

description: Library name: THC0539GPZN_CGGBP1_ChIP1


title: ChIP-seq analysis of MYRFL genomic target locations in HEK293, THC0520TANN_MYRFL_ChIP1

description: Library name: THC0520GPZN_MYRFL_ChIP1


title: ChIP-seq analysis of ZNF578 genomic target locations in HEK293, THC0466TANN_ZNF578_ChIP2

description: Library name: THC0466GPZN_ZNF578_ChIP2


title: Pre-IP control THC0436TANM_TIGD5_INPUT1

description: Library name: THC0436GPZM_TIGD5_INPUT1


title: Pre-IP control THC0394TANM_PRDM13_INPUT1

description: Library name: THC0394GPZM_PRDM13_INPUT1


title: ChIP-seq analysis of KDM5B genomic target locations in HEK293, THC0402TAND_KDM5B_ChIP1

description: Library name: THC0402GPZD_KDM5B_ChIP1


title: Pre-IP control THC0386TAND_ZBTB5_INPUT1

description: Library name: THC0386GPZD_ZBTB5_INPUT1


title: Pre-IP control THC0394TAND_PRDM13_INPUT1

description: Library name: THC0394GPZD_PRDM13_INPUT1


title: ChIP-seq analysis of PRDM5 genomic target locations in HEK293, THC0361TANM_PRDM5_ChIP1

description: Library name: THC0361GPZM_PRDM5_ChIP1


title: ChIP-seq analysis of PRMT3 genomic target locations in HEK293, THC0369TANM_PRMT3_ChIP1

description: Library name: THC0369GPZM_PRMT3_ChIP1


title: ChIP-seq analysis of ZNF14 genomic target locations in HEK293, THC0349TANM_ZNF14_ChIP2

description: Library name: THC0349GPZM_ZNF14_ChIP2


title: ChIP-seq analysis of ZNF280D genomic target locations in HEK293, THC0332TANM_ZNF280D_ChIP2

description: Library name: THC0332GPZM_ZNF280D_ChIP2


title: ChIP-seq analysis of ZNF14 genomic target locations in HEK293, THC0349TAND_ZNF14_ChIP2

description: Library name: THC0349GPZD_ZNF14_ChIP2


title: Pre-IP control THC0386TANM_ZBTB5_INPUT1

description: Library name: THC0386GPZM_ZBTB5_INPUT1


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0306TANM_NCOA1_ChIP1

description: Library name: THC0306GPZM_NCOA1_ChIP1


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0306TAND_NCOA1_ChIP1

description: Library name: THC0306GPZD_NCOA1_ChIP1


title: ChIP-seq analysis of PRMT3 genomic target locations in HEK293, THC0369TAND_PRMT3_ChIP1

description: Library name: THC0369GPZD_PRMT3_ChIP1


title: ChIP-seq analysis of ZNF280D genomic target locations in HEK293, THC0332TAND_ZNF280D_ChIP2

description: Library name: THC0332GPZD_ZNF280D_ChIP2


title: Mouse_iNkx22SDmut_rep2

city: New York

description: Library name: iSD_rep2

value: spinal motor neuron organoid

value: pMN+Nkx22 expression

value: DOX


title: Pre-IP control THC0264TANN_ZBTB5_INPUT1

description: Library name: THC0264GPZN_ZBTB5_INPUT1


title: ChIP-seq analysis of RBSN genomic target locations in HEK293, THC0290TAND_RBSN_ChIP1

description: Library name: THC0290GPZD_RBSN_ChIP1

value: RBSN


title: ChIP-seq analysis of RLF genomic target locations in HEK293, THC0298TANM_RLF_ChIP1

description: Library name: THC0298GPZM_RLF_ChIP1

value: RLF


title: Pre-IP control THC0262TANN_PRDM13_INPUT1

description: Library name: THC0262GPZN_PRDM13_INPUT1


title: ChIP-seq analysis of RBSN genomic target locations in HEK293, THC0290TANM_RBSN_ChIP1

description: Library name: THC0290GPZM_RBSN_ChIP1


title: ChIP-seq analysis of RLF genomic target locations in HEK293, THC0298TAND_RLF_ChIP1

description: Library name: THC0298GPZD_RLF_ChIP1


title: ChIP-seq analysis of ZBTB5 genomic target locations in HEK293, THC0219TANN_ZBTB5_ChIP1

description: Library name: THC0219GPZN_ZBTB5_ChIP1


title: ChIP-seq analysis of AKAP8L genomic target locations in HEK293, THC0163TANN_AKAP8L_CHIP1

description: Library name: THC0163GPZN_AKAP8L_CHIP1

value: CHIP


title: ChIP-seq analysis of ZBTB5 genomic target locations in HEK293, THC0227TANN_ZBTB5_ChIP2

description: Library name: THC0227GPZN_ZBTB5_ChIP2


title: Pre-IP control THC0128TANN_TIGD4_INPUT2

description: Library name: THC0128GPZN_TIGD4_INPUT2


title: ChIP-seq analysis of TIGD4 genomic target locations in HEK293, THC0110TANN_TIGD4_ChIP2

description: Library name: THC0110GPZN_TIGD4_ChIP2


title: ChIP-seq analysis of TIGD5 genomic target locations in HEK293, THC0113TANN_TIGD5_ChIP1

description: Library name: THC0113GPZN_TIGD5_ChIP1


title: ChIP-seq analysis of TIGD5 genomic target locations in HEK293, THC0071TANN_TIGD5_ChIP2

description: Library name: THC0071GPZN_TIGD5_ChIP2


title: siIGF2BP1_replicate1

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

description:
Library name: NB22
IGF2BP1 siRNA-pool transfected

data_processing:
Low-quality read ends and sequencing adapter fragments were trimmed using Cutadapt v2.8.
Reads were aligned to the human genome (UCSC GRCh38) using HISAT2 v2.1.0.
Gene-mapped reads were summarized with FeatureCounts based on Ensembl annotation (GRCh v38.100).
Assembly: GRCh38
Supplementary files format and content: comma separated file containing raw counts

source_name: PDAC

growth_protocol: Transfection for 72 hours

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
poly(A) enrichment, strand-specific library preparation and sequencing was performed by Novogene (Munich).

treatment_protocol: siRNA transfection

value: PDAC

value: PDAC-derived cell line


title: siControl_replicate1

description:
Library name: NB19
control siRNA transfected


title: siIGF2BP1_replicate2

description:
Library name: NB23
IGF2BP1 siRNA-pool transfected


title: siControl_replicate2

description:
Library name: NB20
control siRNA transfected


title: siControl_replicate3

description:
Library name: NB21
control siRNA transfected


title: HeLa cell, HRV-infection, 30 μM of TA25 (TA9) treatment, 48 hpi

city: Chuncheon

first: Bohyeon

last: Kim

state: Gangwon-do

address: Department of Microbiology, College of Medicine Hallym  University 1, Hallimdaehak-gil, Chuncheon-si 24252, Gangwon-  do, Republic of Korea

department: Department of Microbiology

institute: College of Medicine, Hallym University

description: Library name: HRV-B14+TA25

data_processing:
Raw sequencing reads were generated on the Illumina NovaSeq6000 platform as paired-end reads (2 x 100 bp).
Adapter sequences and low-quality bases were removed from raw reads using Fastp.
Trimmed reads were aligned to the reference genome using STAR.
Transcript-level and gene-level quantification was performed using Salmon.
Read count normalization was conducted using CPM and TMM normalization methods implemented in the conorm pipeline.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Raw sequencing data are provided as FASTQ files, and alighned reads are provided as BAM files.
Supplementary files format and content: Tab-delimited text files contain raw read counts and normalized expression values for each gene and isoform per sample.

source_name: human cervical adenocarcinoma cell

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS), 1% HEPES (1 M) and 1% Antibiotic-Antimycotic (Anti-Anti; 100 X). Cells were incubated at 37℃ with 5% CO2.

extract_protocol:
Total RNA from the cells was collected using 1 mL of TRIzol reagent according to the manufacturer's protocol.
RNA libraried for RNA-seq were prepared using the RiboCop rRNA Depletion Kit followed by the CORALL RNA-seq V2 Library Prep Kit according to the manufacturer's instructions.

treatment_protocol: HeLa cells were infected with HRV-B14 at MOI 0.1 at 34℃ with 5% CO2. After 2 h of infection, the cells were treated with 30 μM of TA25. Cells were harvested at 48 hpi.

value: human cervical adenocarcinoma cell

value: HeLa cells

value: epithelial

value: WT

value: 30 μM of TA25 treatment

value: 48 hpi


title: HeLa cell, non-infection, non-treatment, 48 hpi

description: Library name: Mock

value: non-infection and treatment


title: HeLa cell, HRV-infection, non-treatment, 48 hpi

description: Library name: HRV-B14

value: HRV infection


title: Pool2.2

city: Hannover

first: Jenni

last: Fleischauer

address: Carl-Neuberg-Strasse 1

department: Institute of Experimental Hematology

institute: Hannover Medical School

description:
Library name: N3918
total RNA

data_processing:
The 10X Genomics CellRanger analysis pipeline set (v7.0.0) was used with default parameters. Briefly, BCL files were demultiplexed into FASTQ files by cellranger mkfastq using the respective sample sheet with utilized 10X barcodes. The cellranger count pipeline was used to align read data to the reference genome provided by 10X Genomics (Human reference dataset refdata-gex-GRCh38-2020-A), counting aligned reads per gene, and calculating clustering and summary statistics. Subsequently, outputs from cellranger count of all samples were aggregated, normalized to the same sequencing depth, and the feature-barcode matrices were recomputed by cellranger aggr. Simultaneously, feature barcoding data was processed during the cellranger count step with a feature reference build according to the specification of TotalSeq™-B antibodies. The output from cellranger count was demultiplexed to retrieve values for each previously pooled sample. Demultiplexing with hashtag oligos was performed using a Seurat (v.4.0.0) based workflow developed in a collaboration of Dresden-concept Genome Center (TU Dresden) and Research Core Unit Genomics (Hannover Medical School) (https://github.com/ktrns/scrnaseq).
Assembly: Human hg38
Supplementary files format and content: Cellranger output files: N3917_barcodes.tsv.gz, N3917_features.tsv.gz, N3917_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N3918_barcodes.tsv.gz, N3918_features.tsv.gz, N3918_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N6178_barcodes.tsv.gz, N6178_features.tsv.gz, N6178_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N6179_barcodes.tsv.gz, N6179_features.tsv.gz, N6179_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N6180_barcodes.tsv.gz, N6180_features.tsv.gz, N6180_matrix.mtx.gz

source_name: Umbilical cord blood

growth_protocol: Human umbilical cord blood (UCB)-derived hematopoietic stem and progenitor cells (HSPCs) were purified for CD34+CD38-CD45RA- cells and seeded for expansion. The basal medium contains the cytokines SCF, FLT3-L, TPO, and IL-3 in StemSpan SFEM medium. To enhance HSPC expansion, the small molecules A83-01, pomalidomide, and UM171 were added. HSPCs were expanded in most experiments for 7 days, but extended expansion for 14 days was also evaluated.

extract_protocol:
Uncultivated cells were thawed on the day of the run. The expanded HSPCs were harvested directly from culture. Cells were washed with PBS and prepared for Hashtag Oligo (HTO) antibody staining. Therefore, 1x10^6 cells were resuspended in FACS buffer (PBS with 2% FCS, 2 mM EDTA) containing Fc receptor blocking solution for 15 min at 4°C. Then, cells were stained with 0.1 µg antibody/10^6 cells for 30 min at 4°C. Afterwards, the cells were washed 3x with FACS buffer. BioLegend recommends using 5-ml tubes and centrifugation in swing-bucket centrifuges. To exclude dead cells during FACS, we resuspended the cells in FACS buffer with 0.2 µg/ml DAPI. Before the sort, the cells were filtered through a 40-µM cell strainer. We sorted DAPI-negative cells using the FACSAria Fusion cell sorter with a 100-µm nozzle. We started sorting the uncultivated cells (the lowest cell number) and sorted equivalent cell numbers of the other conditions into one tube. Usually, one pool contained five HTO-labelled samples.
Library preparation for single-cell mRNA seq was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 CellSurfaceProtein User Guide (Manual Part Number CG000206 Rev D, 10x Genomics).

treatment_protocol: Human UCB-derived HSPC expansion with APU compounds

value: Umbilical cord blood

tag: library type

value: mRNA


title: T24 cells siTRIM28 replicate 3

city: hefei

first: Dexin

last: Shen

address: lujiang road

institute: university of science and technology of china

description:
Library name: siTRIM28_rep3
RNA-seq of T24 cells transfected with siTRIM28, biological replicate 3

data_processing:
Use Fastp (version 0.23.2) software for data quality control
Sequence reads were trimmed for adaptor sequence/low-quality sequence using by fastp (version 0.23.1)
Trimmed sequence reads were mapped to Ensembl_GRCh38_release113 using STAR(version 2.7.6a) with default parameters.
The featureCounts（version 1.5.1）was used for reads distribution statistic
Assembly: Ensembl_GRCh38_release113
Supplementary files format and content: genes.reads.count.txt: Tab-delimited spreadsheet containing the raw gene-level read count matrix generated by featureCounts. Rows represent genes (gene ID/gene symbol) and columns represent individual RNA-seq libraries (siNC and siTRIM28 biological replicates). Values are integer read counts for each gene in each sample.
Supplementary files format and content: genes.expression.txt: Tab-delimited spreadsheet containing the normalized gene expression matrix derived from the raw counts. Rows represent genes and columns represent samples as above; values are normalized expression values (e.g., TPM/FPKM or other normalized measure as generated in the study).

growth_protocol: The cell lines and culture conditions employed in this study are consistent with those reported in our previous study, as previously reported 15. All cell lines used in this study are obtained from the Cell Bank of the Chinese Academy of Sciences. T24 BLCA cells are maintained in the 1640 medium. All media are supplemented with 10% FBS (Biochannel, BC-SE-FBS08, China) and 1% penicillin-streptomycin (Biochannel, BC-CE-007, China).

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent (Thermo Fisher, cat. no. 15596026) following the manufacturer's recommended protocol.
Polyadenylated RNA enrichment was conducted the total RNA using VAHTS mRNA Capture Beads (Vazyme, China, cat. #N401), following the manufacturer's prescribed protocol. and then components of KCTM Digital Stranded mRNA Library Prep Kit (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction

treatment_protocol: All steps are performed as previously reported 15. KeygenMAX3000 Reagent (KGA9705-1.5, KeyGen BioTECH) are used for nucleic acid transfection.

value: urothelial carcinoma cell line


title: T24 cells siTRIM28 replicate 2

description:
Library name: siTRIM28_rep2
RNA-seq of T24 cells transfected with siTRIM28, biological replicate 2


title: T24 cells siTRIM28 replicate 1

description:
Library name: siTRIM28_rep1
RNA-seq of T24 cells transfected with siTRIM28, biological replicate 1


title: T24 cells siNC replicate 3

description:
Library name: siNC_rep3
RNA-seq of T24 cells transfected with siNC, biological replicate 3

value: siNC


title: T24 cells siNC replicate 2

description:
Library name: siNC_rep2
RNA-seq of T24 cells transfected with siNC, biological replicate 2


title: siIGF2BP1_replicate3

description:
Library name: NB24
IGF2BP1 siRNA-pool transfected


title: Pool1

description:
Library name: N3917
total RNA


title: SAS cell COL17A1 Knockdown (si2)

city: Guangzhou

first: Xiaoxia

last: Wang

state: Guangdong

address: No. 280, Waihuan East Road, Xiaoguwei Sub-district, Panyu District

institute: Guangdong Pharmaceutical University

description:
Library name: SAS_KD_COL17A1
Replicate 1
COL17A1-S2

data_processing:
Raw reads were quality control checked and trimmed to remove adapters and low-quality bases.
Clean reads were aligned to the human reference genome (hg38) using STAR or HISAT2 aligner.
Gene expression levels were quantified (read counts) based on Ensembl gene annotations.
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated. Differential expression analysis was performed using the edgeR package.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Excel spreadsheet containing raw read counts and FPKM normalized values for all genes across all samples.

source_name: Tongue squamous cell carcinoma

growth_protocol: SAS cells were cultured in DMEM supplemented with 10% FBS and antibiotics at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's instructions. RNA quality and quantity were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer.
Total RNA was extracted and quality controlled using Nanodrop and Qubit. mRNA was enriched using Oligo(dT) magnetic beads. Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit (or equivalent). The workflow included mRNA fragmentation, cDNA synthesis using random primers, end repair, A-tailing, adapter ligation, PCR amplification, and purification with AMPure XP beads. Library quality was assessed by Qubit and Agilent Bioanalyzer prior to sequencing.

treatment_protocol: Cells were transfected with Negative Control siRNA or COL17A1-targeting siRNA using Lipofectamine 3000 according to the manufacturer's protocol. Cells were harvested 48 hours post-transfection.

value: Tongue squamous cell carcinoma

value: SAS

value: Epithelial cells

value: Wild type

value: COL17A1 siRNA knockdown


title: ChIP-seq analysis of PRDM5 genomic target locations in HEK293, THC0361TAND_PRDM5_ChIP1

description: Library name: THC0361GPZD_PRDM5_ChIP1

value: ChIP

value: Not approved


title: SAS cell Negative Control

description:
Library name: SAS_Control_NC
Replicate 1
COL17A1-NC

value: Negative Control siRNA


title: OS076

city: Beijing

first: Jichuan

state: Beijing

address: No. 11 Xizhimen South St.

institute: Peking University People's Hospital

description:
Library name: OSPR076
Osteosarcoma tumor sample.

data_processing:
Raw sequencing data were quality-filtered and trimmed.Reads were mapped to the human reference genome (hg38) using STAR (v2.7).Gene-level expression was quantified using featureCounts.Expression data were normalized as FPKM.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing gene-level expression quantified as FPKM.

source_name: primary osteosarcoma

extract_protocol:
Fresh-frozen tumor specimens from 70 patients were processed under sterile con-ditions, immediately cryopreserved in liquid nitrogen, and maintained at -80 °C until analysis. Total RNA isolation was performed using TRIzol reagent (Invitrogen, CA, USA) in accordance with the manufacturer's guidelines. RNA purity and concentration were determined using a NanoDrop 2000 spectropho-tometer (Thermo Fisher Scientific, USA), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Samples with RNA integrity number (RIN)>=7 were subjected to library construction. Sequencing libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, China) according to the manufacturer's instructions, and sequenced on an Illumina NovaSeq 6000 platform generating 150-bp paired-end reads.

value: primary osteosarcoma


title: OS075

description:
Library name: OSPR075
Osteosarcoma tumor sample.


title: OS072

description:
Library name: OSBR072
Osteosarcoma tumor sample.


title: OS074

description:
Library name: OSPR074
Osteosarcoma tumor sample.


title: T24 cells siNC replicate 1

description:
Library name: siNC_rep1
RNA-seq of T24 cells transfected with siNC, biological replicate 1


title: OS077

description:
Library name: OSRR077
Osteosarcoma tumor sample.


title: OS078

description:
Library name: OSRR078
Osteosarcoma tumor sample.


title: OS073

description:
Library name: OSPR073
Osteosarcoma tumor sample.


title: OS069

description:
Library name: OSBR069
Osteosarcoma tumor sample.


title: OS066

description:
Library name: OSBR066
Osteosarcoma tumor sample.


title: OS071

description:
Library name: OSBR071
Osteosarcoma tumor sample.


title: OS065

description:
Library name: OSBR065
Osteosarcoma tumor sample.


title: OS070

description:
Library name: OSBR070
Osteosarcoma tumor sample.


title: OS067

description:
Library name: OSBR067
Osteosarcoma tumor sample.


title: OS068

description:
Library name: OSBR068
Osteosarcoma tumor sample.


title: OS064

description:
Library name: OSBR064
Osteosarcoma tumor sample.


title: OS063

description:
Library name: OSBR063
Osteosarcoma tumor sample.


title: ChIP-seq analysis of ZBTB40 genomic target locations in HEK293, THC0156TANN_ZBTB40_ChIP1

description: Library name: THC0156GPZN_ZBTB40_ChIP1


title: OS046

description:
Library name: OSPR046
Osteosarcoma tumor sample.


title: OS060,B

description:
Library name: OSBR060
Osteosarcoma tumor sample.


title: OS047

description:
Library name: OSRR047
Osteosarcoma tumor sample.


title: OS048

description:
Library name: OSRR048
Osteosarcoma tumor sample.


title: OS060,P

description:
Library name: OSPR060
Osteosarcoma tumor sample.


title: OS049

description:
Library name: OSRR049
Osteosarcoma tumor sample.


title: OS045

description:
Library name: OSPR045
Osteosarcoma tumor sample.


title: OS061

description:
Library name: OSBR061
Osteosarcoma tumor sample.


title: OS042

description:
Library name: OSPR042
Osteosarcoma tumor sample.


title: OS050

description:
Library name: OSRR050
Osteosarcoma tumor sample.


title: OS041

description:
Library name: OSPR041
Osteosarcoma tumor sample.


title: OS062

description:
Library name: OSBR062
Osteosarcoma tumor sample.


title: OS037

description:
Library name: OSPR037
Osteosarcoma tumor sample.


title: OS034

description:
Library name: OSBR034
Osteosarcoma tumor sample.


title: OS031

description:
Library name: OSBR031
Osteosarcoma tumor sample.


title: OS038

description:
Library name: OSPR038
Osteosarcoma tumor sample.


title: OS032

description:
Library name: OSBR032
Osteosarcoma tumor sample.


title: OS039

description:
Library name: OSPR039
Osteosarcoma tumor sample.


title: OS043

description:
Library name: OSPR043
Osteosarcoma tumor sample.


title: OS044

description:
Library name: OSPR044
Osteosarcoma tumor sample.


title: OS040

description:
Library name: OSPR040
Osteosarcoma tumor sample.


title: OS030

description:
Library name: OSBR030
Osteosarcoma tumor sample.


title: OS033

description:
Library name: OSBR033
Osteosarcoma tumor sample.


title: OS028

description:
Library name: OSBR028
Osteosarcoma tumor sample.


title: OS029

description:
Library name: OSBR029
Osteosarcoma tumor sample.


title: OS022

description:
Library name: OSBR022
Osteosarcoma tumor sample.


title: OS019

description:
Library name: OSBR019
Osteosarcoma tumor sample.


title: OS024

description:
Library name: OSBR024
Osteosarcoma tumor sample.


title: OS027

description:
Library name: OSBR027
Osteosarcoma tumor sample.


title: OS026

description:
Library name: OSBR026
Osteosarcoma tumor sample.


title: OS020

description:
Library name: OSBR020
Osteosarcoma tumor sample.


title: OS023

description:
Library name: OSBR023
Osteosarcoma tumor sample.


title: OS079

description:
Library name: OSRR079
Osteosarcoma tumor sample.


title: OS017

description:
Library name: OSBR017
Osteosarcoma tumor sample.


title: OS016

description:
Library name: OSBR016
Osteosarcoma tumor sample.


title: OS014

description:
Library name: OSBR014
Osteosarcoma tumor sample.


title: OS015

description:
Library name: OSBR015
Osteosarcoma tumor sample.


title: OS011

description:
Library name: OSBR011
Osteosarcoma tumor sample.


title: OS013

description:
Library name: OSBR013
Osteosarcoma tumor sample.


title: OS012

description:
Library name: OSBR012
Osteosarcoma tumor sample.


title: OS025

description:
Library name: OSBR025
Osteosarcoma tumor sample.


title: OS009

description:
Library name: OSBR009
Osteosarcoma tumor sample.


title: OS010

description:
Library name: OSBR010
Osteosarcoma tumor sample.


title: OS008

description:
Library name: OSBR008
Osteosarcoma tumor sample.


title: OS006

description:
Library name: OSBR006
Osteosarcoma tumor sample.


title: OS007

description:
Library name: OSBR007
Osteosarcoma tumor sample.


title: OS005

description:
Library name: OSBR005
Osteosarcoma tumor sample.


title: OS004

description:
Library name: OSBR004
Osteosarcoma tumor sample.


title: OS003

description:
Library name: OSBR003
Osteosarcoma tumor sample.


title: OS002

description:
Library name: OSBR002
Osteosarcoma tumor sample.


title: OS001

description:
Library name: OSBR001
Osteosarcoma tumor sample.


title: MV411 cells, DMSO, 48h, rep1

first: hui

last: zeng

address: 106 Zhongshan 2nd Rd

institute: Guangdong Provincial People's Hospital

description: Library name: DMSO_1

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. We use fastp (0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.The reference genome and gene annotation files were downloaded from genome website.The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).We used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.Then difference expression of genes was analyzed by DESeq (v1.38.3).Gene Set Enrichment Analysis (GSEA) (v4.1.0) software was used to perform GSEA enrichment analysis.
Assembly: GRCh38
Supplementary files format and content: CSV file including FPKM for each sample.

extract_protocol:
Total RNA was extracted by the chloroform method.
Three micrograms of RNA were used as the starting material for the RNA sample preparations. The sequencing library was prepared according to the following steps: First, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Next, fragmentation was performed under elevated temperature using divalent cations in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Residual overhangs were converted into blunt ends via exonuclease/polymerase activity, and the enzymes were subsequently removed. After adenylation of the 3' ends of the DNA fragments, Illumina paired-end (PE) adapter oligonucleotides were ligated. To select cDNA fragments of the preferred in length, library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with adapters ligated om both ends were selectively enriched through a 15 cycle PCR reaction using the Illumina PCR Primer Cocktail. The final products were purified with the AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The total concentration of the libraries was measured using the PicoGreen assay (Quantifluor-ST fluorometer, Promega, Madison, Wisconsin, USA, Quant-iT PicoGreen dsDNA Assay Kit, Invitrogen, California, USA). The effective concentration of the libraries was quantified by qPCR (StepOnePlus Real-Time PCR Systems, Thermo Scientific, Waltham, Massachusetts, USA). Multiplexed DNA libraries were normalized and pooled at equal volumes. The pooled library was serially diluted, quantified, and subsequently sequenced in PE150 mode on an Illumina sequencing platform.

value: WT

value: DMSO

tag: time


title: MV411 cells, Corilagin, 48h, rep3

description: Library name: COR_3

value: Corilagin


title: MV411 cells, DMSO, 48h, rep2

description: Library name: DMSO_2


title: OS051

description:
Library name: OSRR051
Osteosarcoma tumor sample.


title: MV411 cells, Corilagin, 48h, rep2

description: Library name: COR_2


title: MV411 cells, Corilagin, 48h, rep1

description: Library name: COR_1


title: OS021

description:
Library name: OSBR021
Osteosarcoma tumor sample.


title: TRIM28_MORC2_CRISPRi_Control_Rep3

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: TRIM28_MORC2_CRISPRi_Control_Rep3

data_processing:
RNAseq Unique mapping (L1 loci mapping): STAR aligner (version 2.7.8a; --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03).
RNAseq Genes were quantified using featureCounts (Subread version 1.6.3), forcing matching strandness of the reads to the features being quantified (-s 2).
RNAseq BAM files were indexed using samtools (version 1.16.1) and converted to bigwig files using deeptools bamCoverage (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Bigwigs for genome browser visualization
Supplementary files format and content: Bulk RNAseq read count matrix for genes

extract_protocol:
Total RNA for bulkRNAseq was isolated using the RNeasy Mini Kit (Quiagen) with on column DNAse treatment following the manufacturer’s instructions. RNA sequencing was performed using 3 biological replicates.
Libraries for RNA sequencing were generated using Illumina TruSeq Stranded mRNA library prep kit (with poly-A selection).

tag: lentivirus

tag: type

value: human neuroepithelial-like stem cells

tag: target gene

value: LacZ


title: TRIM28_CRISPRi_Rep3

description: Library name: TRIM28_CRISPRi_Rep3


title: MV411 cells, DMSO, 48h, rep3

description: Library name: DMSO_3


title: TRIM28_CRISPRi_Rep2

description: Library name: TRIM28_CRISPRi_Rep2


title: TRIM28_MORC2_CRISPRi_Control_Rep2

description: Library name: TRIM28_MORC2_CRISPRi_Control_Rep2


title: TRIM28_MORC2_CRISPRi_Control_Rep1

description: Library name: TRIM28_MORC2_CRISPRi_Control_Rep1


title: MORC2_TRIM28_double_CRISPRi_MOI4_Rep2

description: Library name: MORC2_TRIM28_double_CRISPRi_MOI4_Rep2


title: TRIM28_CRISPRi_Rep1

description: Library name: TRIM28_CRISPRi_Rep1


title: MORC2_CRISPRi_Rep2

description: Library name: MORC2_CRISPRi_Rep2


title: MORC2_TRIM28_double_CRISPRi_MOI4_Rep1

description: Library name: MORC2_TRIM28_double_CRISPRi_MOI4_Rep1


title: MORC2_CRISPRi_Rep1

description: Library name: MORC2_CRISPRi_Rep1