title: LT-HSCs, Piezo1 KO, rep1

description:
Library name: KO1
Total 6 samples were analysed in this study. 3 samples as control, 3 samples as Piezo3 KO groups.

value: Piezo1 knockout


title: CUG11X Nasal cells HIV infected, ART greater than 1 year

status: Public on Nov 03 2025

type: SRA

city: Blantyre

first: Joseph

middle: Aston

last: Phiri

state: Southern Region

address: Chipatala Avenue

country: Malawi

institute: Malawi Liverpool Wellcome Programme

description:
Library name: CUG11X
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data demultiplexing, barcoded cunting, gene counting were made using cellranger count (cellranger version 8.0.1). https://www.10xgenomics.com/support/jp/software/cell-ranger/downloads#download-links
Assembly: Human reference (GRCh38) - 2024-A
Supplementary files format and content: Tab seprated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Inferior turbinate nasal cells

extract_protocol:
Nasal cells collected using nasal currette were dislodged by pipetting liquid up and down the tip of the curette, and cells were centrifuged at 500g for 10 min at 4 °C. The supernatant was completely removed, and cells were resuspended in 500 µl of PBS (Fisher Scientific) counted snd loaded onto a chromium controller.
Single-cell RNA libraries were prepared using the Chromium Next GEM Single Cell 5′ Reagent Kit v2 and Chromium Controller (10× Genomics), following the manufacturer’s protocol. We loaded 10,000-16,000 nasal single-cell suspensions, with a minimum viability greater than 80%, into microfluidic chips to generate Gel Beads-in-Emulsion (GEMs), where individual cells were lysed, and mRNA barcoded using oligo(dT) primers with unique molecular identifiers (UMIs) and cell barcodes. Template switching was facilitated by a template switch oligonucleotide (TSO) to enable full-length cDNA synthesis. GEMs were broken, and barcoded cDNA was recovered and amplified by PCR.

tag: tissue

value: Inferior turbinate nasal cells

tag: cell type

value: Immune, epithelial cells


title: wt 0-1h rep1_pool3

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 661 University Ave

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
Library name: LWG_1h_2_3
Column name in all processed file: LWG_1h.2_3
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt

library_source: transcriptomic

data_processing:
Sequencing adapter trimming and quality control were carried out using Trimgalore (Version 0.6.5) with default parameters
The Drosophila melanogaster 7SLRNA, rRNA, pseudogene-rRNA, tRNA, mtRNA and other species of rRNAs (rRNA_databases, https://github.com/sortmerna/sortmerna/tree/master/data/rRNA_databases) were pre-filtered by sortMeRNA (version 2.1)
The reads were aligned to FlyBase release 6.23 transcriptome RNA (FB2018_04) using Salmon (Version 1.9.1). With corrects for fragment GC-content bias and selective alignment to decoy-aware transcriptome. The whole genome was used as decoy.
TPM and normlized count extraction used the R package tximeta (version 1.20.3) and DEseq2 (version 1.42.1)
Assembly: FlyBase release 6.23 (FB2018_04)
Supplementary files format and content: tab-delimited text file includeDEseq2 normlized count for each sample
Supplementary files format and content: tab-delimited text file include TPM  for each sample

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were kept at 25ºC on a 12 hour light/dark cycle

extract_protocol:
The polysome gradient protocol was adapted from Chen et al., 2014, with modifications. See paper MATERIALS AND METHODS.
RNA libraries were prepared using a NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina and following the manufacturer’s protocol. Ribosomal RNA depletion was performed using the QIAseq FastSelect rRNA Fly Kit (QIAGEN, Cat# 333265 (96 rxns) following the manufacturer’s protocol.

treatment_protocol: Embryos were collected from two groups: orb2∆ZZ and w1118 (pre-injected control). Extract was prepared from embryos collected 0 to 3 hours post egg-lay with 1-hour intervals (0-1h, 1-2h, 2-3h), dechorionated with ice cold 100% bleach for 2 minutes, washed with 0.1% Triton X-100, and disrupted by crushing using 0.5 g embryos per mL of polysome lysis buffer ( 7.5 mM MgCl2, 500 mM NaCl, 25 mM Tris (pH 7.5), 1 mM DTT, 1 mM AEBSF, 2 μg/mL leupeptin, 2 mM benzamidine, 2 μg/mL pepstatin A, 2 mg/mL heparin, 0.5 mg/mL cycloheximide).

value: embryos

tag: time

tag: genotype

value: wild type

tag: treatment

value: 15-45% sucrose gradient


title: LT-HSCs, Control, rep3

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

country: China

institute: Zhejiang University

description:
Library name: Ctr3
Total 6 samples were analysed in this study. 3 samples as control, 3 samples as Piezo2 KO groups.

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file inclueds raw counts for each sample

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using TRIZOL Reagent according to the manufacturer’s instructions (Invitrogen). RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit.
RNA-seq

treatment_protocol: LT-HSCs were sorted from the bone marrow of control and Piezo1 KO mice.

value: Bone marrow

tag: cell line

value: LT-HSCs

value: Bone marrow cells

value: WT


title: LT-HSCs, Control, rep2

description:
Library name: Ctr2
Total 6 samples were analysed in this study. 3 samples as control, 3 samples as Piezo1 KO groups.


title: Tumor_cell_KLG4_2

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

description: Tumor cell_RPKM_of_ALL_Genes_with_Pvalue.xls

data_processing:
Illumina Hiseq X Ten platform for sequencing with 150-bp paired-end reads strategy (Novogene)
Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev)
All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read
Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).
Assembly: Mus_musculus_Ensemble_94
Supplementary files format and content: excel with FPKM for every gene (Rows) and every sample (Columns)

source_name: lungs

extract_protocol:
Tumor cells, TRMs, MDMs, Monocytes and CD8+ T cells were isolated from tumor of KL and KLG4 mice based FACS. the cells were homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lungs

value: primary cells

value: Tumor cells

value: primary cells from tumor lungs 10 weeks after intranasal injection of Ad-Cre and Tamoxifen treatment


title: wt 0-1h rep2_pool1

description:
Library name: LWG_1h_3_1
Column name in all processed file: LWG_1h.3_1
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: CUF13I Nasal cells HIV infected, ART greater than 1 year

description:
Library name: CUF13I
10x Genomics


title: Tumor_cell_KLG4_1


title: LT-HSCs, Control, rep1

description:
Library name: Ctr1
Total 6 samples were analysed in this study. 3 samples as control, 3 samples as Piezo1 KO groups.


title: CUF135 Nasal cells HIV infected, ART greater than 1 year

description:
Library name: CUF135
10x Genomics


title: Tumor_cell_KL_2


title: HCC1937-Doc bio rep 3

city: Xinxiang

first: Xin

last: Zhao

address: Jinsui Avenue

institute: Xinxiang Central Hospital

description:
Library name: HCC1937-Doc-L006
NovaSeq PE150

data_processing:
A quality check was conducted via MultiQC (v1.11). The RNA reads were aligned to the human or mouse reference genome and counted via featureCounts (2.0.1).
Assembly: GRCh38 for human cell line.
Supplementary files format and content: tab-delimited txt file includes raw count for each sample

source_name: Breast

extract_protocol:
Cells were kept in Trizol and RNA was isolated by Novogene.
mRNA library preparation (poly A enrichment) according to the standard protocol

value: Breast

value: Breast cancer cell line


title: HFD-SG34-48-replicate_3

city: kunming

first: shunkai

last: chen

address: wujiaying

department: school of life sciences

institute: Yunnan university

description: Library name: HFD-SG34-48-replicate_3

data_processing:
Sequence reads were trimmed by Trim Galore(v0.6.10)
Clean reads were mapped to GRCm39 using STAR (v2.7.11b)
Read count extraction were performed using featureCounts (v1.6.3)
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.40.2)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene expression for each Sample

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNAs were extracted from embryos at specific stages utilizing TRIzol reagent.  Each RNA sample (500 ng total RNA) underwent rRNA depletion.
Strand-specific libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for ILLUMINA, following the manufacturer's instructions.

value: liver


title: Tumor_cell_KL_1


title: HFD-SG34-48-replicate_2

description: Library name: HFD-SG34-48-replicate_2


title: CUF13K Nasal cells HIV infected, ART less than 3 months

description:
Library name: CUF13K
10x Genomics


title: HCC1937-Doc bio rep 1

description:
Library name: HCC1937-Doc-L004
NovaSeq PE150


title: HFD-SG34-48-replicate_1

description: Library name: HFD-SG34-48-replicate_1


title: HCC1937-Doc bio rep 2

description:
Library name: HCC1937-Doc-L005
NovaSeq PE150


title: M22K_14_16: Liver_Symbiotic vs Obesity.control

type: RNA

city: Juarez

first: Isui Abril

last: Garcia Montoya

state: Chihuahua

address: Plutarco Elias Calles  1210

department: Químico Biológicas

country: Mexico

institute: Universidad Autónoma de Ciudad Juárez

description: RNA equimolar pools from five mice in each group were made.

hyb_protocol: Hybridization was performed using the M22K_01 (UNAM, Mexico City, Mexico) chip containing 23,232 genes from the mouse genome

scan_protocol: The scan and acquisition of the signal were developed using the ScanArray 4000 (Packard BioChips Technologies, Billerica, Massachusetts, USA).

data_processing: The analysis of the microarray scanning was done using GenArise Microarray Analysis Tool software (UNAM), and the lists of differentially expressed genes (DEGs) (Z-score ≥ 2 SD) were obtained

source_name: Liver, obesity, control

label_protocol: Reverse transcription-polymerase chain reaction (RT-PCR) was performed, and the resulting complementary DNA (cDNA) from Normocaloric group was labeled with Cy5, while the cDNA from the Obesity.control group was labeled with Cy3

extract_protocol: Total RNA was purified using TRIzol reagent method extraction, following the manufacturer’s protocol

tag: strain

tag: gender

value: male

tag: obesity model

value: Obesity

value: No treated

value: Liver

source_name: Liver, symbiotic

value: obesity treated

value: Symbiotic diet


title: CFU130 Nasal cells HIV infected, ART greater than 1 year

description:
Library name: CFU130
10x Genomics

value: Inferior turbinate nasal cells

value: Immune, epithelial cells


title: HCC1937-con bio rep 3

description:
Library name: HCC1937-con-L003
NovaSeq PE150


title: CFU134 Nasal cells HIV infected, ART less than 3 months

description:
Library name: CFU134
10x Genomics


title: CUF137 Nasal cells HIV uninfected

description:
Library name: CUF137
10x Genomics


title: HCC1937-con bio rep 2

description:
Library name: HCC1937-con-L002
NovaSeq PE150


title: HFD-replicate_3

description: Library name: HFD-replicate_3


title: wt 0-1h rep1_pool1

description:
Library name: LWG_1h_2_1
Column name in all processed file: LWG_1h.2_1
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt

value: embryos

value: wild type

value: 15-45% sucrose gradient


title: HFD-replicate_2

description: Library name: HFD-replicate_2


title: M22K_14_14: Liver_Normocaloric vs Obesity.control

source_name: Liver, normocaloric

value: Normocaloric diet


title: CUF136 Nasal cells HIV uninfected

description:
Library name: CUF136
10x Genomics


title: CUF13J Nasal cells HIV infected, ART less than 3 months

description:
Library name: CUF13J
10x Genomics


title: KYSE30 Cells YTHDF3 (Input)

city: zhengzhou

first: Xiangyu

last: Wang

state: Henan

address: No. 100 Science Avenue

institute: Zhengzhou University School of Basic Medical Sciences

description: Library name: KYSE30 Cells RIP_Seq_Input

data_processing:
Raw RIP-seq data were quality-controlled, followed by UMI-based deduplication and error correction. Clean reads were mapped to the reference genome, and peaks representing YTHDF3-binding sites were identified by comparing IP and input samples. Peaks were annotated to genomic features, and peak-associated genes were subjected to GO and KEGG enrichment analysis. Motif analysis was also performed to uncover YTHDF3-binding sequence preferences.
Assembly: hg38
Supplementary files format and content: Excel file includes IP peaks for each sample

source_name: Esophageal squamous cell

growth_protocol: KYSE30 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifined atmosphere with 5% CO2 at 37 ℃

extract_protocol:
Cells were lysed to isolate soluble RNA-protein complexes for subsequent immunoprecipitation
RNA from IP and input samples was fragmented and reverse-transcribed into cDNA using random hexamer primers. Unique Molecular Identifiers (UMIs) were added during adapter ligation to enable deduplication. After end repair, adapter ligation, size selection, and PCR amplification, the libraries (~300 bp) were quality-checked and sequenced on the Illumina platform using paired-end 150 bp reads.

treatment_protocol: no

value: Esophageal squamous cell

value: ESCC


title: KYSE30 Cells YTHDF3 (RIP)

description: Library name: KYSE30 Cells RIP_Seq_IP


title: positive-input-ID_S11

status: Public on Nov 02 2025

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
The ChIP-seq data was processed using the following steps: Raw FASTQ files were mapped to the rat genome (rn6) using Bowtie2 (v2.4.5). The resulting SAM files were sorted and indexed with Samtools (v1.15.1). The bigwig files were generated using deepTools (v3.5.1). Peak calling was conducted using MACS2 (v2.2.7.1) with an effective genome size of 2.75 billion, a q-value cutoff of 0.01, with the setting either broad or sharp peak calling. Finally, peak annotation was performed with HOMER.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Rodent tissue samples were diced with a scalpel, washed twice with ice-cold PBS, crosslinked in 1% formaldehyde (15 min in PBS) with frequent vortexing, and quenched with the kit provided formaldehyde quenching solution (Abcam, ab223876; 5 min in PBS) before 2x PBS washes. Crosslinked HeLa cells or rodent tissue was resuspended in 500 µL of Extraction and Lysis Buffer supplemented with protease inhibitors, then treated with 10 passes of both the loose and tight Dounce homogenizer settings, before being incubated for 30 min at RT with 1000 rpm shaking. Chromatin pellets were spun down (10,000 rpm, 15 min) and washed once with milliQ water. Chromatin was then sheared by sonication with a Bioruptor Pico (30s on/30s off, 30 min for tissue), insoluble material was spun down (10,000 g, 10 min) and soluble sheared chromatin was stored at -80 °C.
Immunoprecipitation (IP) Buffer (from Chromatin Extraction Kit, ab223876) was added to the sonicated chromatin (200 µL of sonicated chromatin was added to 2 mL of 1x IP Buffer) followed by 2 µL of A:G Dynabeads (pre-rinsed at least three times with IP Buffer). The mixture was incubated at room temperature for 30 min with mixing at 900 rpm before the supernatant was removed after centrifugation (1 min, 1000 g). To reduce background signal, further addition and incubation with A:G Dynabeads (2 µL) was performed. The mixture was centrifuged and the supernatant collected. Aliquots of the supernatant were taken (2 x 50 µL) for inputs. To 1 mL of cleared chromatin, α-HA (132 ng) or α-H3 (248 ng) antibody was added, and the solution was incubated overnight at 4 °C. A:G Dynabeads (10 µL) were then added and mixed for 5 h at 900 rpm. The supernatant was removed on a magnetic stand. The beads were then resuspended and washed twice with RIPA (radioimmunoprecipitation assay) wash buffer (50 mM HEPES, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) followed by TE (Tris-EDTA) buffer containing 50 mM NaCl (1 mL). The bead solutions were centrifuged (3 min, 1000 g) to remove the TE buffer. The chromatin IP was eluted from the beads with 210 µL of elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS; made fresh) and incubation at 65 °C for 30 min at 900 rpm. The samples were centrifuged (1 min, 16000 g) at room temperature and <200 µL of the desired supernatant was collected. The chromatin supernatant was de-crosslinked overnight at 65 °C. Input samples were diluted with elution buffer (1:4) and similarly, incubated at 65 °C overnight. To the decrosslinked chromatin samples, RNase (1 µL) was added and the mixture was incubated for 1 h at 37 °C (500 rpm). This was then followed by addition of Proteinase K and incubation for 1 h at 45 °C (500 rpm). The DNA was recovered by Qiagen PCR purification kit using standard protocol. Qiagen spin columns were used to bind to the DNA. The DNA was then eluted with 50 – 200 µL of H2O.
The DNA was prepared for sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, E7645) following the manufacturer’s instructions. Briefly, ChIP DNA (~10 ng in 50 µL TE buffer; concentration quantified using a High-sensitivity d1000 TapeStation (Agilent)) were end-repaired, A-tailed and ligated using reagents provided in the kit. Cleanup of the ligation reaction was performed without size selection. The ligated DNA fragments were amplified using indexed primers (Illumina) for 6 PCR cycles and purified with 0.9 x volume NEBNext Sample Purification Beads. Size distribution of the DNA libraries were checked and sequenced using NextSeq 500.

treatment_protocol: Sprague Dawley rats (Charles River, UK), 8–10 weeks of age, were housed under standard diurnal lighting conditions (12 h) with ad libitum access to food and water. All procedures were carried out in accord with the UK Animals (Scientific Procedures) Act (1986) and licensed protocols approved by local committees (LERP and ACER, University of Oxford) and were carried out under licence number P996B4A4E in aseptic conditions. For surgery, the animals were anesthetized in a 2% isoflurane/oxygen mix (2 L min-1) and placed in a stereotactic frame (Stoetling Co., Wood Dale, IL) under maintenance anaesthesia (2.0%) and in accordance with always ARRIVE guidelines. Following isoflurane-induced anaesthesia, the head of the animals was shaved, sterilized, and mounted on a stereotaxic frame. Under an operating microscope, a small midline scalp incision was made after bupivacaine injection and a burr hole was created using a dental drill at 1 mm anterior and 3 mm lateral to the bregma. One microlitre of histone (1 mg mL-1) or vehicle in sterile PBS, was then injected slowly over 5 min via a finely drawn glass microcapillary into the left striatum 4 mm from the cortical surface, before suturing the incision. For control animals, 1 µL of sterile PBS was injected. The animals were allowed to recover from the anaesthesia and were closely monitored throughout and were observed to behave normally before they were returned to their home cage after 5 min. At least 3 animals were used per group in this experiment. Following the injections, the animals were euthanatized with an intraperitoneal injection of sodium pentobarbitone; the brain was removed at either 30 min, 3 h or 6 h and collected either for chromatin extraction or for immunohistochemistry (IHC) after intracardiac perfusion fixation under terminal anaesthesia with 4% paraformaldehyde.

value: Brain

tag: age

value: 8-10 weeks

value: Sprague Dawley rats (Charles River, UK)


title: HCC1937-con bio rep 1

description:
Library name: HCC1937-con-L001
NovaSeq PE150

value: Breast

value: Breast cancer cell line


title: negative-input-ID_S10


title: antiHA-replicate3-ID_S3


title: CFU131 Nasal cells HIV uninfected

description:
Library name: CFU131
10x Genomics


title: antiHA-replicate2-ID_S2


title: antiHA-replicate1-ID_S1


title: antiH3-positive-replicate3-ID_S9


title: antiH3-positive-replicate2-ID_S8


title: antiH3-negative-replicate3-ID_S6


title: M22K_14_15: Liver_Symbiotic vs Normocaloric.control

source_name: Liver, symbiotic, control

value: male

value: Normocaloric

value: No treated


title: antiH3-negative-replicate1-ID_S4


title: ALS patient-derived motor neurons, riluzole treated, donor 8

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

description:
Library name: ALS_iPSCMN_Riluzole_8
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_8

data_processing:
Reads were aligned to human genome build 38 and counts summarized to genes using the Rsubread (v2.12.2) package in the R statistical computing environment v4.2.2 .
Assembly: GRCh38.p13
Supplementary files format and content: tab delimited text files containing raw counts for each sample

source_name: In vitro

growth_protocol: Terminal differentiation of iPSC’s to spinal motor neurons was conducted using small molecules as described in Du et al. Nat Commun (2015). Motor neuron maturation and drug treatment was conducted as described in Bye et al. Nat. Neurosci (2025).

extract_protocol:
Total RNA was isolated from duplicate wells in 48 well plates using an Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) including on-column DNase treatment
RNA libraries were prepared with Illumina Stranded mRNA library preparation kit (Illumina) and sequenced on a NovaSeq 6000 sequencer (Illumina) to approximately 20 million 150 bp paired end reads per sample.

treatment_protocol: Wells were treated with DMSO or Riluzole at Day 36 to a final concentration of 2.5 µM. Media changes of 50% were conducted every 3-4 days containing DMSO/drug at 2.5 µM.

value: In vitro

value: ALS patient-derived iPSC

value: Motor neuon

tag: collection day

value: Riluzole

tag: batch


title: ALS patient-derived motor neurons, riluzole treated, donor 9

description:
Library name: ALS_iPSCMN_Riluzole_9
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_9


title: ALS patient-derived motor neurons, DMSO treated, donor 9

description:
Library name: ALS_iPSCMN_DMSO_9
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_9

value: DMSO


title: ALS patient-derived motor neurons, DMSO treated, donor 8

description:
Library name: ALS_iPSCMN_DMSO_8
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_8


title: HFD-replicate_1

description: Library name: HFD-replicate_1

value: liver


title: ALS patient-derived motor neurons, DMSO treated, donor 6

description:
Library name: ALS_iPSCMN_DMSO_6
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_6


title: ALS patient-derived motor neurons, riluzole treated, donor 4

description:
Library name: ALS_iPSCMN_Riluzole_4
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_4


title: ALS patient-derived motor neurons, DMSO treated, donor 7

description:
Library name: ALS_iPSCMN_DMSO_7
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_7


title: ALS patient-derived motor neurons, DMSO treated, donor 3

description:
Library name: ALS_iPSCMN_DMSO_3
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_3


title: ALS patient-derived motor neurons, DMSO treated, donor 5

description:
Library name: ALS_iPSCMN_DMSO_5
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_5


title: ALS patient-derived motor neurons, riluzole treated, donor 6

description:
Library name: ALS_iPSCMN_Riluzole_6
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_6


title: ALS patient-derived motor neurons, riluzole treated, donor 5

description:
Library name: ALS_iPSCMN_Riluzole_5
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_5


title: ALS patient-derived motor neurons, riluzole treated, donor 2

description:
Library name: ALS_iPSCMN_Riluzole_2
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_2


title: ALS patient-derived motor neurons, DMSO treated, donor 2

description:
Library name: ALS_iPSCMN_DMSO_2
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_2


title: ALS patient-derived motor neurons, DMSO treated, donor 4

description:
Library name: ALS_iPSCMN_DMSO_4
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_4


title: ALS patient-derived motor neurons, riluzole treated, donor 3

description:
Library name: ALS_iPSCMN_Riluzole_3
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_3


title: ALS patient-derived motor neurons, DMSO treated, donor 1

description:
Library name: ALS_iPSCMN_DMSO_1
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_DMSO_1


title: antiH3-positive-replicate1-ID_S7


title: antiH3-negative-replicate2-ID_S5


title: Human CKD+HF plasma EVs sample hp32

city: New York

first: Alex

last: Gallinat

state: NY

address: One Gustave L Levy Place, Box. 1030

department: Cardiovascular Research Institute

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: hp32

data_processing:
The original image data were analyzed using Bcl2fastq for base calling and preliminary quality analysis.
Trimmomatic (v0.30) was used to process the raw data to obtain the clean data for subsequent data analysis.
5’ or 3’ end bases that contains N’s or of quality values below 20, bases with average quality score below 20 using the sliding window of 4bp and reads that are less than 18 bp long after trimming, were also removed
The trimmed reads were mapped to the Homo sapiens GRCh38/hg38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Raw miRNA counts were then corrected for library size differences using a scaling normalization approach. Quantile normalization was then applied to ensure comparable distribution across samples, Log transformation was performed to stabilize variance and approximate normality.
Genes with consistently low expression across samples were removed.
Assembly: GRCh38/hg38
Supplementary files format and content: txt files containing miRNA raw read counts for individual samples.
Supplementary files format and content: Tab-delimited TXT file containing miRNA raw read counts for all samples.

source_name: plasma extracellular vesicles

extract_protocol:
Plasma was isolated from blood collected in sodium citrate tubes and sequentially centrifuged to remove cells, platelets, and microvesicles. Extracellular vesicles (EVs) were isolated via ultracentrifugation (120,000 × g, 90 min), and total RNA was extracted using the miRNeasy micro kit (Qiagen).
Small RNA libraries were prepared using the SMARTer smRNA-seq Kit (Takara Bio). Small RNA sequencing libraries were selected using AMPure beads for corrected size.

value: plasma extracellular vesicles

tag: condition

value: CKD+HF


title: Human CKD+HF plasma EVs sample hp30

description: Library name: hp30


title: Human CKD plasma EVs sample hp28

description: Library name: hp28

value: CKD


title: Human CKD plasma EVs sample hp31

description: Library name: hp31


title: Human CKD plasma EVs sample hp27

description: Library name: hp27


title: Human CKD plasma EVs sample hp26

description: Library name: hp26


title: Human CKD plasma EVs sample hp25

description: Library name: hp25


title: Human CKD plasma EVs sample hp24

description: Library name: hp24


title: ALS patient-derived motor neurons, riluzole treated, donor 7

description:
Library name: ALS_iPSCMN_Riluzole_7
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_7


title: Human CKD plasma EVs sample hp23

description: Library name: hp23


title: Human CKD plasma EVs sample hp22

description: Library name: hp22


title: Human CKD+HF plasma EVs sample hp20

description: Library name: hp20


title: Human CKD+HF plasma EVs sample hp19

description: Library name: hp19


title: Human control plasma EVs sample hp17

description: Library name: hp17

value: Control


title: ALS patient-derived motor neurons, riluzole treated, donor 1

description:
Library name: ALS_iPSCMN_Riluzole_1
Column name in Riluzole_treatment_raw_counts.txt:ALS_iPSCMN_Riluzole_1


title: Human control plasma EVs sample hp16

description: Library name: hp16


title: Human control plasma EVs sample hp15

description: Library name: hp15


title: T12

city: Shanghai

first: Zhuoqing

last: Xu

address: No. 197, Ruijin Er Road, Shanghai,

department: Ruijin Hospital

institute: Department of General Surgery

description:
Library name: T12
GEXSCOP

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colorectal cancer tissue

extract_protocol:
Focal areas of solid and GG components were identified by tissue appearance and compute tomography (CT) at the same time. Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Illumina NovaSeq 6000 with 150 bp paired-end reads.

value: colorectal cancer tissue


title: T8

description:
Library name: T8
GEXSCOP


title: Human control plasma EVs sample hp14

description: Library name: hp14


title: Human control plasma EVs sample hp18

description: Library name: hp18


title: Human control plasma EVs sample hp13

description: Library name: hp13


title: Human CKD plasma EVs sample hp29

description: Library name: hp29


title: T11

description:
Library name: T11
GEXSCOP


title: T10

description:
Library name: T10
GEXSCOP


title: T9

description:
Library name: T9
GEXSCOP


title: T7

description:
Library name: T7
GEXSCOP


title: T5

description:
Library name: T5
GEXSCOP


title: T6

description:
Library name: T6
GEXSCOP


title: T1

description:
Library name: TI
GEXSCOP


title: T4

description:
Library name: T4
GEXSCOP


title: T3

description:
Library name: T3
GEXSCOP


title: 13_HDN_3

description:
Library name: 13HDN-3
High-density neutrophils

data_processing:
Raw reads were filtered to remove the adaptor by cutadapt.
RNAseq reads were aligned to the hg38 genome using NextGenMap.
Read counts for individual gene of each sample were produced with featureCounts.
The differential expression analysis was performed with the DESeq2.
Assembly: hg38
Supplementary files format and content: xlsx(gene expression of all sample)

source_name: Peripheral blood of CRC patients

growth_protocol: Neutrophils were cultured in RPMI-1640 medium containing 10% FBS serum and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
DTT, dNTP, RNase Inhibitor, RT Enzyme and 5x RT Buffer are added to the previous product to synthesize a strand cDNA.  The supernatant was removed by magnetic separation, and single-stranded DNA was removed by adding Exonuclease I and 10x Exonuclease I Buffer. The supernatant was removed by magnetic separation, and the Poly(A) RNA was removed by adding Elution Buffer. The supernatant was removed by magnetic separation. Random primer, 10x Reaction Buffer, enhancer, dNTP and cDNA Extend Polymerase I were used for the two-strand cDNA synthesis.  After removed the supernatant, Elution Buffer was added. Subsequently, DNA beads were added to the supernatant for the fragments recovery. Then 2x HIFI Amplification Mix and index were added and performed PCR Amplification for library fragments. DNA beads were screened for library fragments.

treatment_protocol: High-density neutrophils (HDNs), mature low-density neutrophils (M-LDN), and immature low-density neutrophils (IM-LDN) were isolated from peripheral blood of colorectal cancer (CRC) patients, followed by cell collection and RNA extraction.

value: Peripheral blood of CRC patients

tag: Sex

tag: tumor stage

value: III

value: Neutrophils


title: 13_HDN_2

description:
Library name: 13HDN-2
High-density neutrophils

value: male


title: 13_HDN_1

description:
Library name: 13HDN-1
High-density neutrophils


title: T2

description:
Library name: T2
GEXSCOP


title: Human CKD plasma EVs sample hp21

description: Library name: hp21


title: 12_IMLDN_3

description:
Library name: 12IMLDN-3
immature low-density neutrophils


title: 12_IMLDN_2

description:
Library name: 12IMLDN-2
immature low-density neutrophils


title: 12_IMLDN_1

description:
Library name: 12IMLDN-1
immature low-density neutrophils


title: 12_HDN_3

description:
Library name: 12HDN-3
High-density neutrophils

value: female

value: I


title: 12_HDN_2

description:
Library name: 12HDN-2
High-density neutrophils


title: 12_HDN_1

description:
Library name: 12HDN-1
High-density neutrophils


title: 11_HDN_3

description:
Library name: 11HDN-3
High-density neutrophils


title: 11_HDN_2

description:
Library name: 11HDN-2
High-density neutrophils


title: 11_MLDN_3

description:
Library name: 11MLDN-3
mature low-density neutrophils


title: 11_IMLDN_1

description:
Library name: 11IMLDN-1
immature low-density neutrophils


title: 11_HDN_1

description:
Library name: 11HDN-1
High-density neutrophils


title: 11_IMLDN_3

description:
Library name: 11IMLDN-3
immature low-density neutrophils


title: 9_HDN_1

description:
Library name: 9HDN-1
High-density neutrophils

value: II


title: 11_IMLDN_2

description:
Library name: 11IMLDN-2
immature low-density neutrophils


title: 9_HDN_3

description:
Library name: 9HDN-3
High-density neutrophils


title: 11_MLDN_2

description:
Library name: 11MLDN-2
mature low-density neutrophils


title: 9_HDN_2

description:
Library name: 9HDN-2
High-density neutrophils


title: 9_MLDN_1

description:
Library name: 9MLDN-1
mature low-density neutrophils


title: 8_IMLDN_3

description:
Library name: 8IMLDN-3
immature low-density neutrophils


title: 8_IMLDN_1

description:
Library name: 8IMLDN-1
immature low-density neutrophils


title: 8_IMLDN_2

description:
Library name: 8IMLDN-2
immature low-density neutrophils


title: 9_IMLDN_3

description:
Library name: 9IMLDN-3
immature low-density neutrophils


title: 9_MLDN_2

description:
Library name: 9MLDN-2
mature low-density neutrophils


title: 11_MLDN_1

description:
Library name: 11MLDN-1
mature low-density neutrophils


title: 8_MLDN_2

description:
Library name: 8MLDN-2
mature low-density neutrophils


title: 8_MLDN_3

description:
Library name: 8MLDN-3
mature low-density neutrophils


title: 9_IMLDN_1

description:
Library name: 9IMLDN-1
immature low-density neutrophils


title: 8_MLDN_1

description:
Library name: 8MLDN-1
mature low-density neutrophils


title: 8_HDN_2

description:
Library name: 8HDN-2
High-density neutrophils


title: 8_HDN_3

description:
Library name: 8HDN-3
High-density neutrophils


title: 7_MLDN_3

description:
Library name: 7MLDN-3
mature low-density neutrophils


title: 7_MLDN_1

description:
Library name: 7MLDN-1
mature low-density neutrophils


title: 8_HDN_1

description:
Library name: 8HDN-1
High-density neutrophils


title: 7_IMLDN_1

description:
Library name: 7IMLDN-1
immature low-density neutrophils


title: 5_IMLDN_2

description:
Library name: 5IMLDN-2
immature low-density neutrophils


title: 7_IMLDN_2

description:
Library name: 7IMLDN-2
immature low-density neutrophils


title: 7_MLDN_2

description:
Library name: 7MLDN-2
mature low-density neutrophils


title: 5_IMLDN_3

description:
Library name: 5IMLDN-3
immature low-density neutrophils


title: 9_MLDN_3

description:
Library name: 9MLDN-3
mature low-density neutrophils


title: 5_IMLDN_1

description:
Library name: 5IMLDN-1
immature low-density neutrophils


title: 3_IMLDN_3

description:
Library name: 3IMLDN-3
immature low-density neutrophils


title: 3_IMLDN_2

description:
Library name: 3IMLDN-2
immature low-density neutrophils


title: 3_IMLDN_1

description:
Library name: 3IMLDN-1
immature low-density neutrophils


title: 1_HDN_2

description:
Library name: HDN-2
High-density neutrophils


title: 9_IMLDN_2

description:
Library name: 9IMLDN-2
immature low-density neutrophils


title: 1_HDN_3

description:
Library name: HDN-3
High-density neutrophils


title: 1_HDN_1

description:
Library name: HDN-1
High-density neutrophils


title: GMCSF_P13_3

description: Library name: 13H-GM-3

treatment_protocol: High-density neutrophils (HDNs) were isolated from peripheral blood of colorectal cancer (CRC) patients, divided into PBS-treated control (Ctrl) and GM-CSF-treated (10 ng/mL, 16 h) groups, followed by cell collection and RNA extraction.

value: GM-CSF-treated


title: GMCSF_P12_3

description: Library name: 12H-GM-3


title: GMCSF_P13_2

description: Library name: 13H-GM-2


title: GMCSF_P13_1

description: Library name: 13H-GM-1


title: Ctrl_P13_3

description: Library name: 13H-Ctrl-3

value: PBS-treated


title: Ctrl_P13_2

description: Library name: 13H-Ctrl-2


title: Ctrl_P12_3

description: Library name: 12H-Ctrl-3


title: GMCSF_P12_1

description: Library name: 12H-GM-1


title: GMCSF_P12_2

description: Library name: 12H-GM-2


title: Ctrl_P12_2

description: Library name: 12H-Ctrl-2


title: Ctrl_P12_1

description: Library name: 12H-Ctrl-1


title: 7_IMLDN_3

description:
Library name: 7IMLDN-3
immature low-density neutrophils


title: GMCSF_P11_3

description: Library name: 11H-GM-3


title: GMCSF_P11_2

description: Library name: 11H-GM-2


title: GMCSF_P11_1

description: Library name: 11H-GM-1


title: Ctrl_P11_3

description: Library name: 11H-Ctrl-3


title: Ctrl_P11_1

description: Library name: 11H-Ctrl-1


title: Mer3-His6FLAG3_ChIPseq_4h

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Library name: Sample 2

data_processing:
Reads were aligned to the Saccer2 version (SGD June 2008) of the S. cerevisiae S288C genome, using Bowtie, allowing for 2 mismatches. Reads that matched more than once in the genome or matching to mitochondrial or ribosomal DNA were eliminated from further analysis.
Reads were also aligned to current version of the S. mikatae genome, using Bowtie, and default parameters. Among the aligned reads, those that did not align to S. cerevisiae genome were kept as the spike-in reads.
Reads that aligned to the S. cerevisiae genome but not to the S. mikatae genome were defined as the experimental reads.
Aligned paired-end reads from independent replicates were merged, generating a single Bam file.
Bam files were converted to big wig format using Deeptools bamCoverage, with a step of 10bp and with a scaling factor calculated as the number of experimental reads divided by the number of spike-in reads
Assembly: Saccer2
Assembly: ASM16705v1
Supplementary files format and content: bigwile format files

organism:
Saccharomyces cerevisiae
Saccharomyces mikatae

growth_protocol: For synchronous meiosis, cells were grown in SPS then transferred to sporulation medium. Cells were collected after the indicated time in sporulation medium.

extract_protocol:
Cells were washed twice with cold PBS, and chromatin immunoprecipitation was performed as described (Sanchez et al Methods Mol Biol. 2021;2153:295-306).
Purified DNA was subjected to library preparation using the Accel-NGS 1S Plus DNA Library Kit (1S Unique Dual indexing kit, Cat. No. 19096)

treatment_protocol: 1. 109 cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125 mM glycin for 5 min.

value: yeast cells

tag: cell mixture

value: 90% S. cerevisiae+10% S. mikatae meiotic cells

value: wild-type MER3-His6FLAG3


title: Mer3-8A-His6FLAG3_ChIPseq_3h

description: Library name: Sample 3


title: h_Input_r2

city: Bronx

first: Pabitra

middle: Kumar

last: Parua

address: 1300 Morris Park Avenue, Forchheimer/236

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
150-nucelotides (150-nt) paired-end sequencing (PE150) was performed on NovaSeq 6000. Quality control and adapter trimming of FASTQ (raw sequencing) files were done in Galaxy using FastQC Read Quality reports (Galaxy Version 0.74) and Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.39), respectively. Processed FASTQ files were aligned to the S. pombe or using Bowtie2 (Galaxy Version 2.5.3). Aligned sequences of each biological replicate were fed into MACS239 (Galaxy Version 2.2.9.1) to call peaks from alignment results. Generated “bedgraph treatment” files were converted to bigwig using “Convert BedGraph to BigWig” (Galaxy Version 1.0.1), mean signal was computed using “bigwigCompare” (Galaxy Version 3.5.4). Generated bigwig files were processed using computeMatrix (Galaxy Version 3.5.4) in DeepTools40 to prepare data for plotting heatmaps and/ or profiles of given regions. Heatmap and Metagene plots were generated using “plotHeatmap” (Galaxy Version 3.5.4) and “plotProfile” (Galaxy Version 3.5.4) tools, respectively. The log2 signal ratios were calculated using “bigwigCompare” (Galaxy Version 3.5.4).
ChIP-seq: Trimmed sequencing reads were aligned to the human genome (version b37, hg19) or S. pombe genome using Bowtie2 in Galaxy (Galaxy Version 2.3.4.2). Normalization of the aligned reads was done using ‘bamCoverage’ (Galaxy Version 3.1.2.0.0) by 1) computing and applying scaling factor obtained using aligned sequencing reads of the spike-in reference genome (Saccharomyces cerevisiae, for spike-in samples) and 2) by computing RPKM (reads per kilobase per million) (for the samples without spike-in control).
ChIP-seq: Aligned sequences of each biological replicate were processed separately to identify enriched binding sites using MACS2 callpeak program (Galaxy Version 2.1.1.20160309.6). The resulting bedgraph files were converted to bigwig using ‘Wig/BedGraph-to-bigWig converter’ (Galaxy Version 1.1.1), replicates were combined using ‘Concatenate datasets’ (Galaxy Version 1.0.0).
ChIP-seq: Matrix was computed using ‘computeMatrix’ (Galaxy v.2.3.6.0) in DeepTools to prepare data for plotting heat maps and/or profiles of given regions. The genome-wide distributions, heat maps and metagene plots were created using ‘plotHeatmap’ (Galaxy Version 3.1.2.0.1) and ‘plotProfile’ (Galaxy Version 3.1.2.0.0) tools, respectively. The phospho-over-total signal ratios (log2-ratio) were calculated using ‘bigwigCompare’ (Galaxy Version 3.1.2.0.0). To generate principal component analysis (PCA) plots ‘plotPCA’ (Galaxy Version 3.1.2.0.0) was used.
Assembly: ChIP-seq: Feb 2009 GRCh37/hg19
Assembly: ChIP-seq: Fission yeast (Schizosaccharomyces_pombe_1.1)
Assembly: ChIP-seq: Spike-in control Saccharomyces cerevisiae (April 2011, sacCer3)
Supplementary files format and content: ChIP-seq: processed files are in bigWig format (n = 2 biological replicates).

growth_protocol:
Strains were grown in YES (5% yeast extract, 30% dextrose, 250 mg/l each of adenine, leucine, lysine, histidine and uracil) media at 30°C. New strains were generated by mating or random spore analysis. Correct marker integration was confirmed by PCR.
HCT116 cells cultured in McCoy’s 5A medium with L-glutamine (10-050-CV, Corning) supplemented with 10% Fetal Bovine Serum (FBS, 10437-028, Gibco) and 1x Penicillin-Streptomycin (30-002-Cl, Corning).

extract_protocol:
Briefly, S. pombe cell cultures were grown in YES to an O.D600 of 0.5 – 0.6 and crosslinked with 1% formaldehyde for 15 minutes at room temperature. Crosslinking was terminated by adding 2.5 M glycine to a final concentration of 125 mM for 5 minutes. Cells were pelleted by centrifugation, washed with cold 1x TBS, frozen on dry ice, and stored at -80°C. Cell pellets from 50 ml cultures were resuspended in ChIP lysis buffer I and lysed in a Mini-Beadbeater-16 in the presence of glass beads (0.1 mm diameter) at 4°C for 1 minute (with 1 minute intervals on ice). Lysates were centrifuged at 16,100 x g for 20 minutes at 4°C. Pellets containing chromatin were resuspended in 1 ml ChIP lysis buffer II and transferred to 15 ml polycarbonate tubes. Lysates were sonicated for 30 minutes at 4°C (30 seconds ON, 30 seconds OFF, output setting high) using a water bath sonicator, transferred to new 1.5 ml tubes, and centrifuged at 16,100 x g for 20 minutes at 4°C. 250 – 300 µg of chromatin extract was incubated with antibodies. Extracts from S. cerevisiae strain BY4742 were also prepared in parallel and spiked into each immunoprecipitation (1% of the weight) for normalization
HCT116 cells grown to 50-60% confluence were crosslinked with 1% formaldehyde (BP-531, Fisher Scientific) for 10 min at 25°C. Crosslinking was quenched with 125 mM glycine for 5 min at 25°C. Cells were washed twice with ice-cold PBS and collected into 1 ml of RIPA buffer supplemented with protease and phosphatase inhibitors for each 150-mm dish. Cells were lysed and chromatin sheared by sonication in a Bioruptor at high power, for 5 x 10 min with cycles of 30 sec ON and 30 sec OFF. Lysates were clarified by centrifugation at 20,000 x gav for 20 min at 4°C. Before immunoprecipitation, lysates (~5 x 106 cells per experiment) were pre-cleared with PierceTM Protein A Agarose (20333, Thermo Scientific) for 2 hr at 4°C. Beads were separated by centrifugation at 4000 x gav for 1 min at 4°C. The resulting supernatant was incubated with antibodies for 4 hr at 4°C with constant nutation. In spike-in control experiments, 10% (w/w) of the crosslinked Saccharomyces cerevisiae chromatin was added to the immunoprecipitation reaction.
ChIP-seq: Preparation of multiplexed ChIP-seq libraries from purified immunoprecipitated chromatin and sequencing were performed as described. In brief, the NEBNext Ultra II DNA Library Preparation kit (E7103S) was used to generate libraries using 5-10 ng of input or immunoprecipitated DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina (Set 1, E7335 and Set 2, E7500)).

value: Human colon cancer

tag: treatment (chip_antibody)


title: spo11delta Mer3-His6FLAG3_ChIPseq_3h

description: Library name: Sample 5

value: spo11delta MER3-His6FLAG3


title: h_Cdk9_r2

value: Cdk9 - A11145 - ABClonal


title: Mer3-8A-His6FLAG3_ChIPseq_4h

description: Library name: Sample 4


title: h_Cdk9_r1


title: Ctrl_P13_1

description: Library name: 13H-Ctrl-1

tag: tissue


title: Mer3-His6FLAG3_ChIPseq_3h

description: Library name: Sample 1

tag: cell type


title: Bax/BAK dKO_Day200_Multiome_ATAC

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: baxbak_day200_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq

library_source: genomic single cell

data_processing:
Single cell Multiome: Sequencing results were processed through the Cell Ranger ARC pipeline (10x Genomics) with default parameters. Seurat V4 was used to perform downstream analysis following the standard pipeline.
Assembly: GRCh38
Supplementary files format and content: Cell-by-gene and Cell-by-peak count matrix for each sample as .h5 format

source_name: Retinal Organoid

extract_protocol:
0.01% Nonidet P40 lysis buffer to prepare single nuclei suspension
scATAC-Seq and scRNA-Seq following 10x multiome guideline

value: Retinal Organoid

value: GM25256 iPSC

value: ~200 days

value: Bax/BAK dKO

tag: library type

value: ATAC


title: h_Input_r1


title: Bax/BAK dKO_Day200_Multiome_RNA

description:
Library name: baxbak_day200_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

tag: genotype

value: mRNA


title: KD_E227_F_m22_APOE4KI

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

description: Library name: S47210_Mm_APOEKI_22m_Cortex_E227.tab

data_processing:
Reads are aligned using STAR on mm10
Reads are counted at gene level using --quantMode GeneCounts from STAR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count at gene level for each sample

source_name: Brain cortex

extract_protocol:
RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared from 500 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit, following the manufacturer’s instructions.

treatment_protocol: APOE4 mice were housed under a 12:12 h light–dark cycle with ad libitum water access and were fed isocaloric amounts of control or ketogenic diets for 12 months, from 10 to 22 months of age.

value: Brain cortex


title: Bax/BAK dKO_Day150_Multiome_RNA

description:
Library name: baxbak_day150_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: ~150 days


title: Bax/BAK dKO_Day100_Multiome_ATAC

description:
Library name: baxbak_day100_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq

value: ~100 days


title: KD_E256_M_m22_APOE4KI

description: Library name: S47208_Mm_APOEKI_22m_Cortex_E256.tab


title: Bax/BAK dKO_Day100_Multiome_RNA

description:
Library name: baxbak_day100_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: SD_E228_F_m22_APOE4KI

description: Library name: S47207_Mm_APOEKI_22m_Cortex_E228.tab


title: SD_E251_M_m22_APOE4KI

description: Library name: S47209_Mm_APOEKI_22m_Cortex_E251.tab


title: Bax/BAK dKO_Day50_Multiome_RNA

description:
Library name: baxbak_day50_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: ~50 days


title: Ctrl_P11_2

description: Library name: 11H-Ctrl-2

value: Peripheral blood of CRC patients

value: male

value: III

value: Neutrophils

tag: treatment

value: PBS-treated


title: Bax/BAK dKO_Day50_Multiome_ATAC

description:
Library name: baxbak_day50_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq

tag: cell line


title: SD_E265_F_m22_APOE4KI

description: Library name: S47205_Mm_APOEKI_22m_Cortex_E265.tab


title: SD_E249_F_m22_APOE4KI

description: Library name: S47204_Mm_APOEKI_22m_Cortex_E249.tab


title: KD_E254_M_m22_APOE4KI

description: Library name: S47212_Mm_APOEKI_22m_Cortex_E254.tab


title: Control_Day200_Multiome_RNA

description:
Library name: control_day200_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: WT


title: KD_E207_F_m22_APOE4KI

description: Library name: S47203_Mm_APOEKI_22m_Cortex_E207.tab


title: Control_Day150_Multiome_ATAC

description:
Library name: control_day150_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq


title: SD_E264_M_m22_APOE4KI

description: Library name: S47211_Mm_APOEKI_22m_Cortex_E264.tab


title: Bax/BAK dKO_Day150_Multiome_ATAC

description:
Library name: baxbak_day150_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq


title: Control_Day150_Multiome_RNA

description:
Library name: control_day150_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: KD_E61_F_m22_APOE4KI

description: Library name: S43256_Mm_APOE_Cortex_E61_RNA.tab


title: Control_Day100_Multiome_ATAC

description:
Library name: control_day100_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq


title: SD_E62_F_m22_APOE4KI

description: Library name: S43254_Mm_APOE_Cortex_E62_RNA.tab


title: Control_Day100_Multiome_RNA

description:
Library name: control_day100_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Control_Day50_Multiome_ATAC

description:
Library name: control_day50_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq


title: KD_E59_M_m22_APOE4KI

description: Library name: S43252_Mm_APOE_Cortex_E59_RNA.tab


title: Control_Day50_Multiome_RNA

description:
Library name: control_day50_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: ZYD_1

city: Harbin

first: Peiyan

last: Liu

address: 600 Changjiang Road

institute: Northeast Agricultural University

description: one samples from soybean seeds

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: Glycine soja W05
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Glycine soja

source_name: seed

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: seed


title: KD_E64_M_m22_APOE4KI

description: Library name: S43253_Mm_APOE_Cortex_E64_RNA.tab


title: KD_E53_M_m22_APOE4KI

description: Library name: S43251_Mm_APOE_Cortex_E53_RNA.tab


title: SD_E66_M_m22_APOE4KI

description: Library name: S43250_Mm_APOE_Cortex_E66_RNA.tab


title: Control_Day200_Multiome_ATAC

description:
Library name: control_day200_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq

value: Retinal Organoid


title: ZYD_2

description: one samples from soybean seeds


title: ZYD_V

description: Fresh frozen Spitial transcriptome sequencing

data_processing:
Rawsequencing dta were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to Glycine_soja genome to gene expression count using Space Ranger's default settings
gene expression level of Refseq coding genes were quantified using Space Ranger‘s default settings
Assembly: Glycine_soja
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv.gz:list of gene IDs
Supplementary files format and content: matrix.mtx.gz:gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

extract_protocol:
The sample was sent to Majorbio Bio-pharm,Technology Co., Ltd (Shanghai) for execution Cryosections were cut at 10-µm thickness (Leica, cm1950).
Libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239:https://assets.ctfassets.net/an68im79xiti/3pyXucRaiKWcscXy3cmRHL/a1ba41c77cbf60366202805ead8f64d7/CG000239_VisiumSpatialGeneExpression_UserGuide_Rev_A.pdf).


title: KD_E68_F_m22_APOE4KI

description: Library name: S43257_Mm_APOE_Cortex_E68_RNA.tab


title: KD_E213_M_m22_APOE4KI

description: Library name: S47206_Mm_APOEKI_22m_Cortex_E213.tab


title: ZYD_H


title: ERS group3

first: baicheng

last: kuang

state: China/Hubei province

address: Jiefang Street 1095

institute: Institute of Organ Transplantation,Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
Library name: sample6
Control
ERS3

data_processing:
FeatureCounts (2.0.6) was used to count the reads numbers and then FPKM of each gene was calculated.
Assembly: mm39
Supplementary files format and content: count values for each sample

extract_protocol:
RNA was isolated by Trizol Reagent (Takara, Japan, #9109) following the manufacturer’s procedure, and then converted to cDNA and sequenced.
Following quality control and adaptor removal, sequencing reads were aligned to the reference genome using HISAT2 (2.2.1).

value: beta cell

value: Ctrl

value: none treated


title: SD_E51_M_m22_APOE4KI

description: Library name: S43248_Mm_APOE_Cortex_E51_RNA.tab


title: Hvhsfa3-1-1-1-rep3

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

data_processing:
RNA-seq data were mapped against Morex_V3 genome (Mascher et. al., 2021; https://doi.org/10.1093/plcell/koab077) using STAR version 2.7.10a (Dobin et al., 2013; http://doi.org/10.1093/bioinformatics/bts635).
Quantification at gene level was done using STAR with the –quantMode GeneCounts option.
Assembly: GCA_904849725.1
Supplementary files format and content: Raw gene level read counts

organism: Hordeum vulgare

source_name: Second leaves

growth_protocol: H. vulgare (Golden Promise, referred to as wild type) grains were germinated in glass containers on watered filter paper. Plants were grown under a 16/8 h light/dark cycle at 23/21°C.

extract_protocol:
RNA was extracted from the pooled second leaves of 10 plants per sample per biological replicate. RNA extraction was performed with hot-phenol RNA extraction as described . RNA samples were treated with DNAse I (Thermo Fisher 18047019) and DNAse was removed by performing another hot-phenol RNA extraction on the DNAse-treated samples. For qRT-PCR, DNAse-treated RNA was reverse-transcribed using SuperScript II (Thermo Fisher 18064014) according to manufacturer’s instructions.
RNA was sent to BGI Genomics (China) for quality control, library preparation and sequencing using the DNBseq platform (paired end mode, 2x150bp).

treatment_protocol: Seedlings were exposed to HS treatments 7 d after germination, transferred to soil and grown in a greenhouse. HS treatments were performed on 7 d-old seedlings by exposing them at 44°C for 3 h. For aTT assays, plants were primed by exposing them to 38°C for 120 min 1 h before HS treatment. For maTT assays, plants were primed 2 or 3 d before HS treatment with a two-step acclimation treatment (ACC, 38°C for 2 h, 23°C for 1 h and 44°C for 1 h).

value: Second leaves

value: P+T


title: SD_E58_M_m22_APOE4KI

description: Library name: S43249_Mm_APOE_Cortex_E58_RNA.tab

value: Brain cortex


title: SD_E67_F_m22_APOE4KI

description: Library name: S43255_Mm_APOE_Cortex_E67_RNA.tab


title: Hvhsfa3-1-1-0-rep3

value: P


title: ERS group1

description:
Library name: sample4
Control
ERS1


title: ERS group2

description:
Library name: sample5
Control
ERS2


title: Hvhsfa3-1-0-1-rep3

value: T


title: hucMSC-EVs treated group3

description:
Library name: sample3
hucMSC-EVs treated
EVs3

value: EVs treated

value: hucMSC-EVs treated


title: Hvhsfa3-1-0-0-rep3

value: NHS


title: Hvhsfa2-1-1-1-rep3


title: hucMSC-EVs treated group1

description:
Library name: sample1
hucMSC-EVs treated
EVs1


title: hucMSC-EVs treated group2

description:
Library name: sample2
hucMSC-EVs treated
EVs2


title: Cdk9_ubp8{delta}_r2

organism: Schizosaccharomyces pombe

source_name: yeast

value: yeast

value: h+ cdk9-13myc::kanMX6 ubp8{delta}::ura4

value: Myc (9E10) - 626802 - Biolegend


title: Hvhsfa2-1-1-0-rep3


title: Hvhsfa2-1-0-1-rep3


title: Cdk9_ubp8{delta}_r1


title: Wildtype-1-0-rep3

value: Wildtype


title: Pol II_ubp8{delta}_r2

value: Pol II (8WG16) - 664906 - Biolegend


title: A3_T_R2

description: Library name: A3_T_R2

extract_protocol:
RNA was extracted from the pooled second leaves of 10 plants per sample per biological replicate. RNA extraction was performed with hot-phenol RNA extraction as described . RNA samples were treated with DNAse I (Thermo Fisher 18047019) and DNAse was removed by performing another hot-phenol RNA extraction on the DNAse-treated samples. For qRT-PCR, DNAse-treated RNA was reverse-transcribed using SuperScript II (Thermo Fisher 18064014) according to manufacturer’s instructions.
RNA paired-end sequencing was performed at Novogene.


title: A3_T_R1

description: Library name: A3_T_R1


title: Wildtype-0-1-rep3


title: Input_ubp8{delta}_r1


title: Pol II_ubp8{delta}_r1


title: Wildtype-0-0-rep3


title: A3_PT_R1

description: Library name: A3_PT_R1


title: A3_PT_R2

description: Library name: A3_PT_R2


title: A3_N_R3

description: Library name: A3_N_R3


title: pSpt5_htb1K119R_r2

value: htb1-K119R-FLAG::kanMX6 spt5-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M21X h?

value: pSpt5 - Pr1357 - 21st Century Biochemicals


title: A3_N_R1

description: Library name: A3_N_R1


title: A2xA3_T_R3

description: Library name: A2xA3_T_R3

value: Hvhsfa2-1 Hvhsfa3-1


title: A3_N_R2

description: Library name: A3_N_R2


title: pSpt5_htb1K119R_r1


title: Hvhsfa3-1-1-0-rep2


title: A2xA3_T_R1

description: Library name: A2xA3_T_R1


title: Hvhsfa3-1-1-1-rep2


title: Spt5_htb1K119R_r2


title: A2xA3_T_R2

description: Library name: A2xA3_T_R2


title: A2xA3_PT_R3

description: Library name: A2xA3_PT_R3


title: Spt5_htb1K119R_r1


title: Hvhsfa3-1-0-0-rep2


title: A2xA3_PT_R2

description: Library name: A2xA3_PT_R2


title: Wildtype-1-1-rep3


title: A3_PT_R3

description: Library name: A3_PT_R3


title: A3_T_R3

description: Library name: A3_T_R3


title: Cdk9_htb1K119R_r2

value: htb1-K119R-FLAG::kanMX6 cdk9-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h?


title: A2xA3_PT_R1

description: Library name: A2xA3_PT_R1

value: Second leaves


title: Hvhsfa2-1-0-1-rep2


title: A2xA3_N_R3

description: Library name: A2xA3_N_R3


title: Cdk9_htb1K119R_r1


title: A2xA3_N_R2

description: Library name: A2xA3_N_R2


title: Hvhsfa2-1-0-0-rep2


title: A2xA3_N_R1

description: Library name: A2xA3_N_R1


title: Pol II_htb1K119R_r2


title: Pol II_htb1K119R_r1


title: A2_T_R2

description: Library name: A2_T_R2


title: H9c2 cells, Ctrl_1

city: Weifang

first: Peng

state: Shandong Province

address: No. 7166, Bao Tong West Street

institute: Shandong Second Medical University

description: Library name: Ctrl1

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean  reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Assembly: mRatBN7.2
Supplementary files format and content: csv files include TPM values for each Sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

value: cardiomyocytes

value: Ctrl


title: A2_T_R3

description: Library name: A2_T_R3


title: H9c2 cells, Ctrl_3

description: Library name: Ctrl3


title: Hvhsfa2-1-1-1-rep2

value: P+T


title: Wildtype-1-1-rep2


title: H9c2 cells, MMA_FA_2

description: Library name: MMA_FA2


title: Input_htb1K119R_r1


title: A2_PT_R2

description: Library name: A2_PT_R2


title: Wildtype-1-0-rep2

value: P


title: H9c2 cells, MMA_FA_1

description: Library name: MMA_FA1


title: A2_PT_R1

description: Library name: A2_PT_R1


title: A2_T_R1

description: Library name: A2_T_R1

value: T


title: pSpt5_r2

value: cdk9T120G::kanMX6 spt5-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-


title: H9c2 cells, MMA_FA_3

description: Library name: MMA_FA3


title: Wildtype-0-1-rep2


title: A2_N_R3

description: Library name: A2_N_R3

value: NHS


title: H9c2 cells, FA_2

description: Library name: FA2

value: FA


title: A2_PT_R3

description: Library name: A2_PT_R3


title: Wildtype-0-0-rep2


title: H9c2 cells, FA_1

description: Library name: FA1


title: Spt5_r2

value: yeast


title: Hvhsfa3-1-0-1-rep2


title: H9c2 cells, Ctrl_2

description: Library name: Ctrl2


title: Hvhsfa3-1-1-1-rep1


title: Dis2_r2

value: dis2-3FLAG::natMX6 h-

value: FLAG - F3165-1MG - SIGMA


title: H9c2 cells, FA_3

description: Library name: FA3


title: Hvhsfa3-1-1-0-rep1


title: Spt5_r1

value: Myc (9E10) - 626802 - Biolegend


title: A2_N_R2

description: Library name: A2_N_R2


title: pSpt5_r1


title: H9c2 cells, MMA_2

description: Library name: MMA2

value: MMA


title: Input_htb1K119R_r2


title: GP_T_R3

description: Library name: GP_T_R3

value: Wildtype


title: A2_N_R1

description: Library name: A2_N_R1


title: Pch1_r2

value: pch1-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M216 h


title: Hvhsfa3-1-0-0-rep1


title: H9c2 cells, MMA_3

description: Library name: MMA3


title: Hvhsfa2-1-1-1-rep1


title: Dis2_r1


title: Hvhsfa3-1-0-1-rep1


title: htb1-K119R_rep2

description: Library name: htb1-K119R_rep2

data_processing:
ChIP-seq: 150-nucelotides (150-nt) paired-end sequencing (PE150) was performed on NovaSeq 6000. Quality control and adapter trimming of FASTQ (raw sequencing) files were done in Galaxy using FastQC Read Quality reports (Galaxy Version 0.74) and Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.39), respectively. Processed FASTQ files were aligned to the S. pombe or using Bowtie2 (Galaxy Version 2.5.3). Aligned sequences of each biological replicate were fed into MACS239 (Galaxy Version 2.2.9.1) to call peaks from alignment results. Generated “bedgraph treatment” files were converted to bigwig using “Convert BedGraph to BigWig” (Galaxy Version 1.0.1), mean signal was computed using “bigwigCompare” (Galaxy Version 3.5.4). Generated bigwig files were processed using computeMatrix (Galaxy Version 3.5.4) in DeepTools40 to prepare data for plotting heatmaps and/ or profiles of given regions. Heatmap and Metagene plots were generated using “plotHeatmap” (Galaxy Version 3.5.4) and “plotProfile” (Galaxy Version 3.5.4) tools, respectively. The log2 signal ratios were calculated using “bigwigCompare” (Galaxy Version 3.5.4).
RNA-seq: Paired-end sequencing (150 nt, PE150) was conducted by Admera Health. Raw FASTQ files underwent quality control and adapter trimming using the Galaxy platform. Read quality was assessed with FastQC (Galaxy v0.74), and adapters were trimmed using Trimmomatic (Galaxy v0.39). Cleaned reads were aligned to the S. pombe reference genome (ASM294v2) using HISAT2 (Galaxy v2.2.1+galaxy1). Aligned BAM files were then processed with bamCoverage (Galaxy v3.5.4+galaxy0) to generate normalized coverage tracks in bigWig format.
ChIP-seq: Spike-in control Saccharomyces cerevisiae (April 2011, sacCer3)
Assembly: ChIP-seq: Fission yeast (Schizosaccharomyces_pombe_1.1)
Assembly: RNA-seq: S. pombe reference genome (ASM294v2)
Supplementary files format and content: ChIP-seq: Processed files are in bigWig format (n = 2 biological replicates)
Supplementary files format and content: RNA-seq: Processed files are in bigWig format (n = 2 biological replicates)

source_name: Fission yeast

growth_protocol: Strains were grown in YES (5% yeast extract, 30% dextrose, 250 mg/l each of adenine, leucine, lysine, histidine and uracil) media at 30°C. New strains were generated by mating or random spore analysis. Correct marker integration was confirmed by PCR.

extract_protocol:
ChIP-seq: Briefly, S. pombe cell cultures were grown in YES to an O.D600 of 0.5 – 0.6 and crosslinked with 1% formaldehyde for 15 minutes at room temperature. Crosslinking was terminated by adding 2.5 M glycine to a final concentration of 125 mM for 5 minutes. Cells were pelleted by centrifugation, washed with cold 1x TBS, frozen on dry ice, and stored at -80°C. Cell pellets from 50 ml cultures were resuspended in ChIP lysis buffer I and lysed in a Mini-Beadbeater-16 in the presence of glass beads (0.1 mm diameter) at 4°C for 1 minute (with 1 minute intervals on ice). Lysates were centrifuged at 16,100 x g for 20 minutes at 4°C. Pellets containing chromatin were resuspended in 1 ml ChIP lysis buffer II and transferred to 15 ml polycarbonate tubes. Lysates were sonicated for 30 minutes at 4°C (30 seconds ON, 30 seconds OFF, output setting high) using a water bath sonicator, transferred to new 1.5 ml tubes, and centrifuged at 16,100 x g for 20 minutes at 4°C. 250 – 300 µg of chromatin extract was incubated with antibodies. Extracts from S. cerevisiae strain BY4742 were also prepared in parallel and spiked into each immunoprecipitation (1% of the weight) for normalization.
RNA-seq: S. pombe cultures were grown to an OD₆₀₀ of ~0.5. Cells were harvested by centrifugation, flash-frozen on dry ice, and stored at –80°C. Pellets were resuspended in 1 mL QIAzol and lysed using a Mini-Beadbeater-16 with glass beads at 4°C for 1 minute per cycle (with 1-minute intervals on ice) for a total of 5 cycles. Total RNA was extracted using the miRNeasy Micro Kit (Qiagen #1071023), following the manufacturer’s instructions. RNA quantity and purity were assessed using a NanoDrop 2000 spectrophotometer. One microgram (1 μg) of total RNA was reverse-transcribed into cDNA using the SuperScript III First-Strand Synthesis Kit (Invitrogen #18080-051) with random hexamer primers
ChIP-seq: Preparation of multiplexed ChIP-seq libraries from purified immunoprecipitated chromatin and sequencing were performed as described. In brief, the NEBNext Ultra II DNA Library Preparation kit (E7103S) was used to generate libraries using 5-10 ng of input or immunoprecipitated DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina (Set 1, E7335 and Set 2, E7500).
RNA-seq: 1 μg of total RNA from each sample was used to prepare strand-specific libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S), according to the manufacturer’s protocol. After poly(A) selection and fragmentation, first and second strand cDNA synthesis was performed. The resulting double-stranded cDNA was purified using SPRIselect beads (Beckman Coulter #B23317). Adaptors were diluted 5-fold and used for ligation, followed by size selection (~200 nt) using SPRIselect beads. Libraries were enriched by PCR amplification (10 cycles) using NEBNext Ultra II Q5 Master Mix, Universal PCR Primer, and Index (i7) Primers (NEB #E7335S). Final libraries were purified with SPRIselect beads, and their concentration and quality were assessed using Qubit Fluorometric Quantitation and the Bioanalyzer High Sensitivity DNA Kit, respectively.

value: Fission yeast

value: h- ade6-M216 htb1-K119R-FLAG::kanMX6 cdk9-13myc::kanMX


title: Cdk9_rep2

value: cdk9-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+


title: GP_PT_R3

description: Library name: GP_PT_R3

value: Second leaves


title: Hvhsfa2-1-0-1-rep1


title: H9c2 cells, MMA_1

description: Library name: MMA1

value: cardiomyocytes


title: GP_T_R2

description: Library name: GP_T_R2


title: GP_T_R1

description: Library name: GP_T_R1


title: htb1-K119R_rep1

description: Library name: htb1-K119R_rep1


title: Pch1_r1


title: GP_PT_R2

description: Library name: GP_PT_R2

value: P+T


title: Wildtype-1-1-rep1


title: Cdk9_rep1


title: ubp8delta_rep1

description: Library name: ubp8delta_rep1

value: h+ cdk9-13myc::kanMX ubp8delta::ura4


title: Pol II_rep2

value: cdk9T120G::kanMX6 spt5-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-

value: Pol II (8WG16) - 664906 - Biolegend


title: ubp8delta_rep2

description: Library name: ubp8delta_rep2


title: GP_PT_R1

description: Library name: GP_PT_R1


title: Wildtype-0-1-rep1

value: T


title: wt_rep2

description: Library name: wt_rep2


title: Input_r2

value: yeast


title: GP_N_R2

description: Library name: GP_N_R2

value: NHS


title: GP_N_R3

description: Library name: GP_N_R3


title: wt_rep1

description: Library name: wt_rep1


title: Wildtype-0-0-rep1


title: Wildtype-1-0-rep1

value: P


title: Pol II_rep1


title: Hvhsfa2-1-1-0-rep1


title: Input_r1


title: Hvhsfa2-1-0-0-rep1


title: GP_N_R1

description: Library name: GP_N_R1


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 2

status: Public on Nov 01 2025

type: genomic

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description:
SG2_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient

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

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

data_processing:
RnBeads version 2.20.0 on R 4.3.2
beta_dpval_allprobes.txt

label: Cy3 and Cy5

source_name: Noncancerous gastric mucosa

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the standard phenol–chloroform procedure

tag: disease state

value: Gastric cancer

value: Male

value: Noncancerous gastric mucosa


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 1

description:
SG1_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient

value: Female


title: Tumor of post-eradication gastric cancer patient 1

description:
SG1_T
Tumor of post-eradication gastric cancer patient

source_name: Tumor

value: Tumor


title: Tumor of post-eradication gastric cancer patient 2

description:
SG2_T
Tumor of post-eradication gastric cancer patient


title: Tumor of post-eradication gastric cancer patient 13

description:
SG13_T
Tumor of post-eradication gastric cancer patient


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 15

description:
SG15_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: EXP-2

city: Turin

first: Massimo

middle: E

last: Maffei

state: Italy

address: Via Quarello 15/a

department: Life Sciences and Systems Biology

institute: University of Turin

description: Data in the matrix table are expressed as Log2FC of Treatment (Cy5) vs. Control (Cy3)

hyb_protocol: Scanned on an Agilent Technologies Scanner G2505B US45102883

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: CONTROL not exposed

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: Arabidopsis plants grown in vertical squared Petri plates using a headspace co-cultivation. In the upper part plants in the lower part Pseudomonas sytingae DC 3000. Control plates do not contain P. syringae DC3000.

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: ecopyte

tag: days

source_name: TREATMENT mVOC exposed

tag: ecotype


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 12

description:
SG12_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: Tumor of post-eradication gastric cancer patient 11

description:
SG11_T
Tumor of post-eradication gastric cancer patient


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 13

description:
SG13_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: EXP-3


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 6

description:
SG6_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: EXP-4


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 11

description:
SG11_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: Tumor of post-eradication gastric cancer patient 12

description:
SG12_T
Tumor of post-eradication gastric cancer patient


title: Tumor of post-eradication gastric cancer patient 6

description:
SG6_T
Tumor of post-eradication gastric cancer patient


title: EXP-1


title: Tumor of post-eradication gastric cancer patient 10

description:
SG10_T
Tumor of post-eradication gastric cancer patient


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 10

description:
SG10_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: Noncancerous gastric mucosa of post-eradication gastric cancer patient 3

description:
SG3_N
Noncancerous gastric mucosa of post-eradication gastric cancer patient


title: Decidua, normal, 7

city: Daejeon

first: Tae Lyun

last: Ko

address: 245, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Institute of Science and Technology Information

description: Library name: norm_Endo7

data_processing:
Sequencing data were aligned and quantified using Cell Ranger v5.0.0 (10X Genomics) against the human reference genome (GRCh38) provided by Cell Ranger
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Decidua

extract_protocol:
Decidual tissues were collected via dilation and curettage, and single-cell suspensions were prepared by mechanical and enzymatic dissociation.
Single-cell RNA libraries were prepared using the Chromium Single Cell 3′ Library Kit (10X Genomics) according to the manufacturer’s instructions and sequenced on Illumina HiSeq-X and NovaSeq 6000 platforms.

value: Decidua

tag: gestational week

tag: disease

value: Normal


title: HCT116 cells, AMA, 0h

city: Chengdu

first: Jiaqiang

last: Deng

state: Sichuan

address: No.24, South Section 1, 1st Ring Road

institute: Sichuan university

description:
Library name: Sample 7
Column name in raw_counts.txt: D1

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Leveraging the OmicStudio cloud platform for data analysis
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: The cells were maintained in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated from cells via the RNAiso Plus Reagent (Takara). The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: HCT116 cells treated with mtROS inducers(Men (32 μM), 4-HPR (10 μM), or AMA (10 μM)  for 12 h.

value: colon cancer cell

value: AMA

tag: time


title: HCT116 cells, Men, 12h

description:
Library name: Sample 4
Column name in raw_counts.txt: B2

value: Men


title: HCT116 cells, 4-HPR, 0h

description:
Library name: Sample 5
Column name in raw_counts.txt: C1


title: HCT116 cells, 4-HPR, 12h

description:
Library name: Sample 6
Column name in raw_counts.txt: C2


title: HCT116 cells, DMSO, 0h

description:
Library name: Sample 1
Column name in raw_counts.txt: A1

value: DMSO


title: HCT116 cells, Men, 0h

description:
Library name: Sample 3
Column name in raw_counts.txt: B1


title: Control hiPSC-derived esophageal progenitor cell 1

first: Yosuke

last: Mitani

state: New York

address: 1130 St Nicholas Ave, 3rd floor

department: HICCC

institute: Columbia University

description:
Library name: 3-1-A
column name: 3-1-A

data_processing:
Raw reads were assessed for quality using FastQC. Adaptor sequences and low-quality bases were trimmed using Trimmomatic.
Trimmed reads were aligned to the Homo sapiens genome (GRCh38) using STAR aligner.
Aligned reads were counted using featureCounts.
FPKM values were calculated by Azenta Life Sciences using a standard method.
Assembly: GRCh38
Supplementary files format and content: CSV files contain gene-level raw counts (raw_counts.csv) and normalized expression values (normalized_counts.csv) across all samples.

source_name: esophageal progenitor cell

growth_protocol: BU3 NGST hiPSCs were cultured on Matrigel in mTeSR Plus medium under hypoxic conditions and passaged every 5–7 days. Differentiation began with seeding in mTeSR + Y-27632, followed by treatment with the STEMdiff Definitive Endoderm Kit (days 1–3). Cells were then cultured in SFD medium with SB431542 (10uM), Noggin (200 ng/mL), and hEGF (100 ng/mL) during days 4–6, and switched to normoxia on day 7. From days 7–16, SFD medium containing SB431542, Noggin, and increased 200 ng/mL hEGF was used. On days 16, cells were dissociated and FACS-sorted for EpCAM+, NKX2.1-GFP– populations.

extract_protocol:
RNA was isolated using the RNAqueous Total RNA Isolation Kit (Invitrogen, AM1912) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences using a standard mRNA-Seq protocol, following the manufacturer’s instructions. Sequencing was performed on the Illumina platform with 2×150 bp paired-end reads.

treatment_protocol: STAT3 knockout hiPSCs were generated by nucleofecting BU3 NGST cells with Cas9 RNP complexes containing two gRNAs. Colonies were picked, expanded, and screened for STAT3-targeted indels by qRT-PCR and Western blot. Three validated homozygous STAT3 KO clones were used for EPC differentiation, showing consistent phenotypes.

value: esophageal progenitor cell

value: hIPSC

value: Isotype control

value: Esophageal differentiation


title: Control hiPSC-derived esophageal progenitor cell 2

description:
Library name: 3-1-B
column name: 3-1-B


title: STAT3 KO hiPSC-derived esophageal progenitor cell 1

description:
Library name: 1-15-A
column name: 1-15-A


title: PLC-MAP2-2

city: Kong Kong

first: Ut Kei

last: Lou

address: Room 17, 1/F, Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: Sample5
Column name in PLC-normalized read counts.csv: PLC-MAP2-2

data_processing:
Sequencing reads pre-processed and filtered for adapter sequence and low quality sequence, followed by retaining only reads with read length ≥ 40bp.
Sequencing reads were aligned to the Hg38 reference genome using STAR (version 2.7.8).
Raw count was calculated using EBSeq (version 1.18.0).
Assembly: Hg38
Supplementary files format and content: CSV file includes normalized read counts for each sample.

growth_protocol: MHCC97L and PLC/PRF/5 HCC cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin in 37ºC incubator with 5% CO2.

extract_protocol:
RNA were harvested using the RNeasy Kit (Qiagen) according to the manufacturer's protocol.
Libraries were sequenced on a NovaSeq 6000. 1µg total RNA was used for poly-A mRNA library preparation using KAPA mRNA HyperPrep Kit (KR1352-v3.16) according to the manufacturer's instruction. Libraries were sequenced on a NovaSeq 6000.

treatment_protocol: MAP2 was stably knocked out or overexpressed by lentiviral CRISPR-mediated gene knockout and gene activation respectively.

value: Hepatocellular carcinoma

value: MAP2 overexpression


title: Control hiPSC-derived esophageal progenitor cell 3

description:
Library name: 3-1-C
column name: 3-1-C


title: PLC-SAMv2

description:
Library name: Sample4
Column name in PLC-normalized read counts.csv: PLC-SAMv2

value: Empty vector control


title: 97L-sgMAP2-3

description:
Library name: Sample3
Column name in 97L-normalized read counts.csv: 97L-sgMAP2-3

value: MAP2 knockout


title: HCT116 cells, AMA, 12h

description:
Library name: Sample 8
Column name in raw_counts.txt: D2


title: HCT116 cells, DMSO, 12h

description:
Library name: Sample 2
Column name in raw_counts.txt: A2


title: 97L-sgMAP2-2

description:
Library name: Sample2
Column name in 97L-normalized read counts.csv: 97L-sgMAP2-2


title: 97L-sgEV

description:
Library name: Sample1
Column name in 97L-normalized read counts.csv: 97L-sgEV

value: Scramble control


title: STAT3 KO hiPSC-derived esophageal progenitor cell 3

description:
Library name: 1-15-C
column name: 1-15-C


title: NA4EP300 Wildtype

city: New Brunswick

first: Advaitha

last: Madireddy

state: NJ

address: Little Albany Street

institute: Rutgers Cancer Institute

description: Library name: 15A UT

data_processing:
Illumina NovaSeq 6000
Differential analysis was performed using DEseq2 by Active Motif
Gene Ontology was performed using differential genes.
Assembly: hg38
Supplementary files format and content: Differential gene expression in a .txt file
Supplementary files format and content: Gene ontology processed data in a .txt file

source_name: NA-ATLL

growth_protocol: Cells were cultivated in IMDM medium supplemented with 20% human serum, 1% penicillin/streptomycin, and 100 unit/ml IL-2.

extract_protocol:
Trizol extraxtion followed by RNAeasy Qiagen Kit
Activemotif library preperation protocol- Illumina TruSeq RNA Sample Preparation v2 Guide (Illumina)

value: NA-ATLL

value: T-Lymphocyte

value: Wildtype

value: UT


title: NA1EP300 Wildtyp + JQAD1

description: Library name: 4A JQAD1

value: Mutant

value: JQAD1 treated


title: NA3EP300 Mutant

description: Library name: 6A UT


title: STAT3 KO hiPSC-derived esophageal progenitor cell 2

description:
Library name: 1-15-B
column name: 1-15-B


title: hTERT in vitro PDAC CAF cell line, BxPC3-co-cultured, donor 4

city: South San Francisco

first: Elysia

middle: Cecilia

last: Saputra

state: CA

address: 213 E Grand Ave

department: Data, AI, and Genome Sciences

institute: Merck & Co., Inc.

description:
Library name: htertdonor4_coculture
10x Genomics

data_processing:
The demultiplexing of sequencing reads, gene counting, and generation of gene expression matrices were performed using the 10X Genomics Cell Ranger v7.0.1 software. Quality control, normalization, library integration, and subtype identification were performed using Seurat 4.1.1.
Assembly: Human hg38
Supplementary files format and content: RDS objects

growth_protocol: Tumor samples were fragmentized (37 degrees C, 30 minutes with rotation, 10mL RPMI 10% FBS with collagenase and DNAsel), and then the tumor digest was filtered with 70 mm filter. After repeated washing with RPMI until tumor fragments disappear, the collected samples was spun (300 g, 5 minutes), and cell pellets were resuspended in 1 mL FGM-2 BulletKit media and incubated (37 degrees C, 48 hours). Remaining cells were washed with PBS, and with daily replenishment of fresh media, colonies of fibroblasts appeared after 7-10 days. The colonies were expanded in T175 flasks after they reached 7% confluency.

extract_protocol:
0.05% Accutase (trypsin) was used to harvest the cells.
Libraries were constructed using the 10X Chromium single-Cell 3’ reagent v3.1 and 5’ reagent v2 kit per the manufacturer’s protocol. Briefly, single-cell suspensions was mixed with 10X RT reaction master mix, and then loaded together with gel beads and partitioning oil into a 3’ or 5’ Chip. The chip was then loaded onto a chromium controller for single-cell GEM generation and barcoding. RNA transcripts were captured by poly(dT) primers and barcoded with cell barcodes and unique molecular identifiers. After emulsion disruption, cDNA molecules were amplified, followed by fragmentation, adapter, and sample indices addition. The final libraries were quantified with qubit assay, examined by Agilent Tape station, and sequenced by Illumina Novaseq 6000.

treatment_protocol: The cell lines were then either treated with 10ng/mL TGFb1, co-cultured with BxPC3 with 1:1 ratio, or hTERT-immortalized and then co-cultured with BxPC3 with 1:1 ratio.

value: hTERT immortalized PDAC CAF cell lines

value: BxPC3-CAF 1:1 co-culturing


title: hTERT in vitro PDAC CAF cell line, BxPC3-co-cultured, donor 3

description:
Library name: htertdonor3_coculture
10x Genomics


title: hTERT in vitro PDAC CAF cell line, BxPC3-co-cultured, donor 2

description:
Library name: htertdonor2_coculture
10x Genomics


title: In vitro PDAC CAF cell line, BxPC3-co-cultured, donor 3

description:
Library name: donor3_coculture
10x Genomics

value: PDAC CAFs


title: hTERT in vitro PDAC CAF cell line, BxPC3-co-cultured, donor 1

description:
Library name: htertdonor1_coculture
10x Genomics


title: NA2EP300 Mutant

description: Library name: 5A UT


title: NA1EP300 Wildtype

description: Library name: 4A UT


title: In vitro PDAC CAF cell line, BxPC3-co-cultured, donor 1

description:
Library name: donor1_coculture
10x Genomics


title: In vitro PDAC CAF cell line, BxPC3-co-cultured, donor 4

description:
Library name: donor4_coculture
10x Genomics


title: In vitro PDAC CAF cell line, BxPC3-co-cultured, donor 2

description:
Library name: donor2_coculture
10x Genomics


title: In vitro PDAC CAF cell line, TGFb1-treated, donor 4

description:
Library name: donor4_TGFB1
10x Genomics

source_name: PDAC CAFs


title: In vitro PDAC CAF cell line, TGFb1-treated, donor 3

description:
Library name: donor3_TGFB1
10x Genomics


title: In vitro PDAC CAF cell line, TGFb1-treated, donor 2

description:
Library name: donor2_TGFB1
10x Genomics


title: In vitro PDAC CAF cell line, TGFb1-treated, donor 1

description:
Library name: donor1_TGFB1
10x Genomics


title: In vitro PDAC CAF cell line, untreated, donor 4

description:
Library name: donor4_Untreated
10x Genomics


title: In vitro PDAC CAF cell line, untreated, donor 2

description:
Library name: donor2_Untreated
10x Genomics


title: In vitro PDAC CAF cell line, untreated, donor 3

description:
Library name: donor3_Untreated
10x Genomics


title: In vitro PDAC CAF cell line, untreated, donor 1

description:
Library name: donor1_Untreated
10x Genomics


title: Sh-Sy5y cells, Negative Control ChIP, Replicate 2

city: Beer sheva

first: Debra

last: Toiber

state: Beer sheva

address: David Ben Gurion Blvd 1

department: Life Sciences

country: Israel

institute: Ben Gurion University of the Negev

description: Library name: Sh-Sy5y_Cneg_ChIP_rep2

data_processing:
BWA Mapper, Samtools, bamCoverage_Genome, bedClip, bedGraphToBigWig
Trim Galore was used  with --length 25, we also used multiQC
macs3 peakcalling -g hs -f BED --nomodel p 0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: CNS

growth_protocol: DMEM, 10% fetal bovine serum, 2 mM L-glutamine, 1x penicillin/streptomycin. Cultured at 37 °C at 5% CO2, humidified atmosphere.

extract_protocol:
The cells were plated for all the experimental conditions at an equal confluence, fixed with 1% formaldehyde for 10 minutes, quenched, and collected. After, cell pellet resuspension in RIPA buffer, the lysates were sonicated using a vibracell needle sonicator (Sonics & Materials Inc, USA) to break the chromatin. Chromatin immunoprecipitations were carried out using anti-myc antibodies coated magnetic beads (MedChemExpress, Cat# HY-K0206) to isolate Sirt6-bound DNA.
Chip-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science starting from 1-20ng of DNA as previously described (Blecher-Gonen R et al. Nat. prot. (2013)). Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Novaseq 6000 instrument (Illumina) using an SP 100 cycles kit, allocating 20M reads per sample (paired end sequencing).

treatment_protocol: untreated

value: CNS

value: Neuroblastoma cell line

value: untransduced


title: Sh-Sy5y cells, Sirt6 ChIP Input, Replicate 1

description: Library name: Sh-Sy5y_Sirt6_Inp_rep1

value: cMyc-Sirt6 transduction


title: Sh-Sy5y cells, Negative Control ChIP, Replicate 1

description: Library name: Sh-Sy5y_Cneg_ChIP_rep1


title: Sh-Sy5y cells, Negative Control ChIP, Replicate 3

description: Library name: Sh-Sy5y_Cneg_ChIP_rep3