title: gCeO_bRG4_RNA-Seq

description: Library name: 190915

data_processing:
sequence data files were created with bclconvert 4.4.6
RNA-seq libraries were mapped and de-duplicated using STAR with default settings and each libraries was aligned to the human (hg38) and gorilla (gorGor6) reference separately. Gene-level read counts were generated using STAR (--quantMode GeneCounts) during alignment.
Assembly: hg38/gorGor6
Supplementary files format and content: G_count_table_hg38.tsv.gz: Raw gene counts for chimpanzee RNA-seq samples mapped to hg38
Supplementary files format and content: G_count_table_gorGor6.tsv.gz: Raw gene counts for chimpanzee RNA-seq samples mapped to gorGor6

growth_protocol: iPSC line grown under standard conditions (5 % CO2, 37 °C) on Matrigel-coated plates in StemFlex. Cerebral organoids were generated as whole spheres using the STEMdiff Cerebral Organoid Kit or equivalent self-made medium based on previous publications with small modifications as described in detail (Lancaster & Knoblich, 2014; Giandomenico, Sutcliffe & Lancaster, 2021). Briefly, 9,000 cells were seeded into 96-well Ultra-Low Attachment plates and cultured in mTeSR1 containing 10 µM Y-27632 rho kinase inhibitor. Plates were spun for 3 min at 300x g to settle cells. After 48 hours, the medium was changed to mTeSR1 without Y-27632 rho kinase inhibitor (organoid formation medium). On day 4, the now-formed embryoid bodies (EBs) were changed to neural induction medium. EBs were embedded in Matrigel on day 8, transferred to differentiation medium containing B27 supplement without vitamin A (expansion medium), and henceforth cultured on an orbital shaker. Starting on day 14, young organoids were changed to, and then maintained in, differentiation medium containing B27 supplement with vitamin A (maturation medium), changed every 2–3 days until collection for experiments. All cerebral organoids were collected for experiments on w8 ± 3 days.

extract_protocol:
RNA extraction was performed as per the manufacturer’s instructions using the Zymo QuickRNA FFPE MiniPrep Kit
libraries were prepared using the SmartSeq 2 protocol, modified from Picelli et al. 2013. Isolated total RNA from 10,000 cells was denatured for 3 min at 72 °C in 4 μL hypotonic buffer (0.2 % Triton X-100) in the presence of 2.4 mM dNTPs, 240 nM dT-primer and 4 U RNase Inhibitor (NEB). Reverse transcription was performed at 42 °C for 90 min after filling up to 10 µL with RT buffer mix for a final concentration of 1x Superscript II buffer, 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer, 9 U RNase inhibitor and 90 U Superscript II Reverse Transcriptase. The reverse transcriptase was inactivated at 70 °C for 15 min. For subsequent PCR amplification of the cDNA, the optimal PCR cycle number was determined with an aliquot of 1 μL unpurified cDNA in a 10 μL qPCR containing 1x KAPA HiFi Hotstart Readymix, 1x SYBR Green I and 0.2 μM UP primer. The determined cycle number was then used to amplify the residual 9 μL cDNA using 1x KAPA HiFi HotStart Readymix and 250 nM UP-primer under the following cycling conditions: initial denaturation at 98 °C for 3 min, 12–17 cycles [98 °C 20 sec, 67 °C 15 sec, 72 °C 6 min] and final elongation at 72 °C for 5 min. The amplified cDNA was purified using 0.6x Sera-Mag SpeedBeads and resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. cDNA quality and concentration were determined using the FragmentAnalyzer NGS 1-6000bp Kit.  For library preparation, 2 µL amplified cDNA was tagmented in 1x Tagmentation Buffer using 0.8 µL bead-linked transposome (Illumina) at 55 °C for 15 min in a total volume of 4 µL. The reaction was stopped by the addition of 1 µL 0.1 % SDS (37 °C, 15 min), beads were bound to a magnet and the supernatant was removed. Beads were then resuspended in 14 µL indexing PCR Mix containing 1x KAPA Hifi HotStart Ready Mix and 700 nM unique dual indexing primers (i5 and i7), and subjected to a PCR (72 °C 3 min, 98°C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72 °C 5 min). Libraries were purified with 0.9x volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6x and 0.9x. Repurification with a final 0.9x bead purification was performed if needed. Sequencing was performed after quantification using the FragmentAnalyzer NGS 1-6000bp Kit (Agilent) on a NovaSeq S4 v1.5 200 cycles flow cell (Illumina) to a sequencing depth of at least 50 million 100 bp paired-end reads per library.


title: gCeO_N3_RNA-Seq

status: Public on Aug 04 2026

type: SRA

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

country: Germany

institute: TUD Dresden University of Technology

description: Library name: 190913

library_source: transcriptomic

molecule: total RNA

organism: Gorilla gorilla gorilla

source_name: cerebral organoid

tag: tissue

value: cerebral organoid

tag: cell line

tag: cell type

value: BCL11B+ neuron


title: gCeO_bRG3_RNA-Seq

description: Library name: 190911

value: basal radial glia


title: gCeO_aRG3_RNA-Seq

description: Library name: 190910

value: apical radial glia


title: gCeO_bIP2_RNA-Seq

description: Library name: 190909

value: basal intermediate progenitor cell


title: gCeO_bRG2_RNA-Seq

description: Library name: 190908


title: gCeO_N1_RNA-Seq

description: Library name: 190906


title: gCeO_bRG1_RNA-Seq

description: Library name: 190904


title: WT-mid

city: Hongkong

first: Xin

last: Deng

state: 九龍

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

department: BMS

country: Hong Kong

institute: City University of Hong Kong

description:
Library name: WT-mid
RNA-seq

library_source: genomic

data_processing:
Quality-filtered paired reads were mapped to the reference genome, and gene-level quantification was performed using featureCounts (Subread v2.0.1) against annotated features. The resulting count matrix was analyzed using DESeq2 (v1.40.2).
Assembly: Genome assembly ASM585424v1
Supplementary files format and content: The bed file for each DAP-seq displayed the TF binding sites. The counts txt files contained the gene expression counts for each RNA-seq.

molecule: genomic DNA

organism: Klebsiella pneumoniae

source_name: Klebsiella pneumoniae

growth_protocol: LB at 37 °C

extract_protocol:
Total RNA was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen, # Gdp430) and depleted of rRNA using NEBNext® rRNA Depletion Kit (Bacteria) (NEB, #E7850).
Libraries were constructed with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, #E7770L) and sequenced on the Illumina Xten platform.

value: Klebsiella pneumoniae

value: strain

value: genotype

tag: genotype

value: WT

tag: treatment


title: WT-stat

description:
Library name: WT-stat
RNA-seq


title: Mouse GZF1 full length

type: protein

city: rehovot

first: irina

last: miodownik

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Microarray was double-stranded using Thermo Sequenase polymerase and corresponding primers.

scan_protocol: GenePix 4400A array scanner using PMTGain =  700 and ScanPower = 70

data_processing: For each probe area, the median intensity of pixels was calculated. Then, spatial correlation was removed.

label: Alexafluor

molecule: protein

organism: Mus musculus

source_name: recombinant plasmid

label_protocol: FLAG-tag Alexa Fluor.

extract_protocol: Protein expressed with the NEB PURExpress transcription-translation commercial kit.

tag: tag

value: FLAG


title: gCeO_aRG1_RNA-Seq

description: Library name: 190903


title: Mouse Gzf1 full length

scan_protocol: GenePix 4400A array scanner using PMTGain = 550 and ScanPower = 60


title: R9-stat

description:
Library name: R9-stat
RNA-seq


title: R9-mid

description:
Library name: R9-mid
RNA-seq


title: G7-stat

description:
Library name: G7-stat
RNA-seq


title: G7-mid

description:
Library name: G7-mid
RNA-seq


title: F3-stat

description:
Library name: F3-stat
RNA-seq


title: A7-stat

description:
Library name: A7-stat
RNA-seq


title: F3-mid

description:
Library name: F3-mid
RNA-seq


title: A7-mid

description:
Library name: A7-mid
RNA-seq


title: kp-24h

description:
Library name: kp-24h
RNA-seq


title: kp-9h

description:
Library name: kp-9h
RNA-seq


title: kp-4h

description:
Library name: kp-4h
RNA-seq


title: control-lane5

description:
Library name: control-lane5
DAP-seq

value: ChIP antibody

tag: batch


title: control-lane2

description:
Library name: control-lane2
DAP-seq


title: control-lane3

description:
Library name: control-lane3
DAP-seq


title: control-lane1

description:
Library name: control-lane1
DAP-seq


title: T8

description:
Library name: T8
DAP-seq


title: T7

description:
Library name: T7
DAP-seq


title: T6

description:
Library name: T6
DAP-seq


title: T4

description:
Library name: T4
DAP-seq


title: T5

description:
Library name: T5
DAP-seq


title: T3

description:
Library name: T3
DAP-seq


title: T1

description:
Library name: T1
DAP-seq


title: gCeO_aRG4_RNA-Seq

description: Library name: 190914


title: T2

description:
Library name: T2
DAP-seq


title: gCeO_bIP3_RNA-Seq

description: Library name: 190912


title: S9

description:
Library name: S9
DAP-seq


title: S6

description:
Library name: S6
DAP-seq


title: S5

description:
Library name: S5
DAP-seq


title: gCeO_aRG2_RNA-Seq

description: Library name: 190907


title: S4

description:
Library name: S4
DAP-seq


title: S3

description:
Library name: S3
DAP-seq


title: S20

description:
Library name: S20
DAP-seq


title: gCeO_bIP1_RNA-Seq

description: Library name: 190905


title: S2

description:
Library name: S2
DAP-seq


title: S19

description:
Library name: S19
DAP-seq


title: S18

description:
Library name: S18
DAP-seq


title: S17

description:
Library name: S17
DAP-seq


title: S13

description:
Library name: S13
DAP-seq


title: S12

description:
Library name: S12
DAP-seq


title: S11

description:
Library name: S11
DAP-seq


title: S10

description:
Library name: S10
DAP-seq


title: S1

description:
Library name: S1
DAP-seq


title: D137 RPE,CMV>ASCL1-GFP

city: Seattle

first: Thomas

middle: A.

last: Reh

state: WA

address: 1959 NE Pacific Street

department: Neurobiology and Biophysics

country: USA

institute: University of Washington

description: Library name: SCR213_CMV-ascl1-gfp

library_source: transcriptomic single cell

data_processing:
Cellranger count was used for read alignment and counting. All analyses of the resulting count matrices and plotting of results was done in R  using the Seurat package .
Assembly: GRCh38
Supplementary files format and content: h5 file containing sparse count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: retina

growth_protocol: Human fetal eyes of gestational ages between 70 to 150 days were received from the Birth Defects Research Laboratory at the University of Washington following the approved protocol. After the removal of cornea, lens and retina, the remaining tissue consisting of sclera, choroid and RPE was incubated in 0.1 U/µl Collagenase IV (Gibco, 17104019) in HBSS (Gibco, 14025134) at 37 °C for 10 min. RPE was carefully peeled away in coherent sheets from the choroid making sure to avoid carryover of vasculature. RPE sheets were incubated for 15 min in 0.2 U/µl Collagenase IV in HBSS at 37 °C for 10-15 min and subsequently titruated with a P1000 pipette until a suspension of small clumps of ~ 20 cells was achieved. Cells were spun down for 5 min. at 300g, supernatant was removed and pellet resuspended in prewarmed retinal differentiation medium (RDM). Cells were seeded into wells of a 24 well plate (1 ml/well) containing Matrigel (Corning, 354234) coated coverslips. RDM consisted in general of 50% DMEM (Gibco, 12430062), 50% DMEM/F12 (Gibco, 11330032), 1% antibiotic/antimycotic (Millipore Sigma, A5955-100ML), 1% NEAA (Gibco, 11140050), 1-10% FBS (Corning, 35-011-CV), 2% B27 (Gibco, 17504044). For the first experiment cells were isolated from a donor of gestational day 137 (D137) and cultured in RDM with 10% FBS until processing for scRNAseq or staining. For all following experiments we used RDM with 5 % dialyzed FBS (Gibco, 26400044) and B27 without Vitamin A (Gibco, 12587010) from plating until the day of infection when we reduced the FBS concentration to 1%.

extract_protocol:
Single cell RNAseq libraries were prepared using 10x Genomics’ Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (10x Genomics, PN-1000268) according to manufacturer’s protocol.
Single cell RNAseq libraries were prepared using 10x Genomics’ Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (10x Genomics, PN-1000268) according to manufacturer’s protocol.

treatment_protocol: CMV-ASCL1-NEUROD1 overexpression was performed on a D115 sample, which was infected at DIV8 and harvested for scRNAseq or immunostaining on DIV28. After infection, half the wells were treated with 50 ng/ml bFGF (R&D Systems, 3718-FB-025) and 10 µM Activin A inhibitor (SB431542 Gibco, 120-14E-10UG).

value: retina

value: retinal pigment epithelium


title: D137 RPE, no virus

description: Library name: SCR214_nCTRL


title: D137 RPE, Hes1>ASCL1-GFP

description: Library name: SCR212_hes1-ascl1_gfp


title: R9

description:
Library name: R9
DAP-seq


title: D137 RPE, Hes1>GFP

description: Library name: SCR211_hes1-gfp


title: R8

description:
Library name: R8
DAP-seq


title: R7

description:
Library name: R7
DAP-seq


title: R6

description:
Library name: R6
DAP-seq


title: kp-2h

description:
Library name: kp-2h
RNA-seq


title: R5

description:
Library name: R5
DAP-seq


title: supernatant zinc-adequate (ZA) cells rep4

type: RNA

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

hyb_protocol: Hybridization to Gene Chip plate arrays

scan_protocol: Scaning and imaging on Gene Titan Multi-Channel Instrument

data_processing: Statistical data analysis and visualization was performed using R, version 4.3.2 (R Core Team, 2020). The raw data (CEL files) were normalized and summarized using the RMA (robust multiarray average) algorithm from the R package oligo version 1.66.0. The genes were associated with vendor-provided annotation information [Release 36 (Thermofisher)] and control genes were removed after background correction. Moreover, irrelevant genes with low or unchanged expression were removed so that 17,286 probes corresponding to 15,997 genes remained (intensity > 3 in at least 2 samples). Differential gene expression analysis was performed by the R package limma version 3.58.1 (Ritchie, 2015). Linear models were fit and moderated t-statistics were computed by the eBayes function. Afterwards, the Benjamini-Hochberg correction was applied to exclude false-positive results, and thus differentially expressed genes with an adjusted p-value < 0.05 and absolute log2FC > 0.5 were considered significant.

label: biotin

source_name: cell supernatant from zinc-adequate (ZD) cells

label_protocol: The samples were labeled with a GeneChip WT Plus labeling kit at Eurofins (Comp. No. 7230-GT0028).

growth_protocol: 5*10^5 cells were seeded in 6-well plates. Medium was changed either to CTR or ZA and ZD medium the other day. Cells were cultured for an additional 13 days.

extract_protocol: Cell pellets were sent to Eurofins, where extraction of mRNA was conducted.

treatment_protocol: 24 h before ending the experiment, cells cultured in CTR medium were either treated with IL-8, supernatant of cells treated with ZA or ZD medium or CTR medium.

value: intestinal goblet cells

value: supernatant zinc-adequate


title: control-lane4

description:
Library name: control-lane4
DAP-seq


title: supernatant zinc-adequate (ZA) cells rep3


title: supernatant zinc-adequate (ZA) cells rep2


title: R4

description:
Library name: R4
DAP-seq


title: supernatant zinc-adequate (ZA) cells rep1


title: supernatant zinc-deficient (ZD) cells rep4

source_name: cell supernatant from zinc-deficient (ZD) cells

value: supernatant zinc-deficient


title: R20

description:
Library name: R20
DAP-seq


title: R3

description:
Library name: R3
DAP-seq


title: R2

description:
Library name: R2
DAP-seq


title: supernatant zinc-deficient (ZD) cells rep2


title: R18

description:
Library name: R18
DAP-seq


title: R19

description:
Library name: R19
DAP-seq


title: supernatant zinc-deficient (ZD) cells rep1


title: supernatant zinc-deficient (ZD) cells rep3


title: R17

description:
Library name: R17
DAP-seq


title: IL-8 treatment rep3

source_name: cells treated with IL-8


title: IL-8 treatment rep4


title: R16

description:
Library name: R16
DAP-seq


title: R15

description:
Library name: R15
DAP-seq


title: IL-8 treatment rep2


title: IL-8 treatment rep1


title: R14

description:
Library name: R14
DAP-seq


title: R13

description:
Library name: R13
DAP-seq


title: R12

description:
Library name: R12
DAP-seq


title: R11

description:
Library name: R11
DAP-seq


title: zinc-deficient (ZD) rep3

source_name: cells treated with zinc-deficient (ZD) medium

value: zinc-deficient


title: zinc-deficient (ZD) rep2


title: zinc-deficient (ZD) rep4


title: zinc-deficient (ZD) rep1


title: R1

description:
Library name: R1
DAP-seq


title: R10

description:
Library name: R10
DAP-seq


title: zinc-adequate (ZA) rep 4

source_name: cells treated with zinc-adequate (ZA) medium

value: zinc-adequate


title: zinc-adequate (ZA) rep3


title: Q9

description:
Library name: Q9
DAP-seq


title: zinc-adequate (ZA) rep2


title: Q8

description:
Library name: Q8
DAP-seq


title: Poly(I:C)-treated H19-T Ki67-eGFP-negative LT-HSCs, replicate 3

city: Tianjin

first: Shuangshuang

last: Pu

state: China

address: 288 Nanjing Road

country: China

institute: State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases Institute of Hematology

description:
Library name: Sample 30
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: TN_3

data_processing:
Raw paired-end reads were processed using fastp v0.23.1. Read pairs were removed when either read contained adapter contamination, more than 10% undetermined bases, or more than 50% bases with Phred quality scores below 5. Clean reads were aligned to the Mus musculus GRCm38/mm10 reference genome using HISAT2. Alignment files were converted to BAM format, name-sorted, and filtered to remove unmapped reads using SAMtools. Gene-level unnormalized read counts were generated using HTSeq-count with the Ensembl Mus musculus GRCm38.101 annotation.
Raw single-end reads were processed to remove reads containing adapter contamination, poly-N sequences, homopolymeric sequences, low-quality bases, or reads lacking the expected 3′ adapter or insert sequence. Clean reads within the selected small-RNA length range were retained for downstream analysis. Clean reads were mapped to the Mus musculus GRCm38/mm10 reference genome using Bowtie. Seed-based alignment was performed using a 20-nt seed, allowing no more than one mismatch within the seed region. Mapped reads were annotated against known mouse miRNA sequences in miRGeneDB 2.1 and used to quantify known miRNAs.
Assembly: GRCm38/mm10
Supplementary files format and content: 32D_H19_Adar_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A.
Supplementary files format and content: ckit_h19_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for 12 bulk RNA-seq libraries generated from primary mouse c-Kit-positive cells expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant.
Supplementary files format and content: AN_GN_TN_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from poly(I)-treated Ki67-eGFP-negative LT-HSCs carrying H19-A, H19-G, or H19-T alleles.
Supplementary files format and content: miRNA_pulldown_raw_counts.tsv.gz contains gene-level unnormalized read counts for 12 RNA-seq libraries generated from input and biotinylated miRNA pulldown fractions of 32D cells transfected with scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics.
Supplementary files format and content: ki67_eGFP_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for six bulk RNA-seq libraries generated from steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs.
Supplementary files format and content: miRNA_RCadj_libraryRPM.tsv.gz contains reverse-complement-adjusted miRNA abundance values for 21 small RNA-seq libraries. The matrix includes 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A, and primary mouse c-Kit-positive cells expressing empty vector, H19-A, H19-G, or H19-T.

source_name: bone marrow

growth_protocol: 32D and 32D-LV-H19 mouse myeloid progenitor cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 10 ng/mL recombinant mouse interleukin-3, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Primary mouse c-Kit-positive hematopoietic progenitor cells were isolated from bone marrow by magnetic enrichment using CD117 MicroBeads (Miltenyi Biotec). Cells were cultured in serum-free expansion medium supplemented with 100 ng/mL stem cell factor, 100 ng/mL thrombopoietin, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Mice were maintained under specific-pathogen-free conditions. Bone marrow cells were collected from 8- to 10-week-old female mice. LT-HSCs were identified and purified by fluorescence-activated cell sorting using the Lin⁻Sca-1⁺c-Kit⁺CD34⁻Flt3⁻ phenotype. In Ki67-eGFP reporter mice, Ki67-eGFP-negative LT-HSCs were defined as quiescent cells, whereas Ki67-eGFP-positive LT-HSCs were defined as cycling cells.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. Samples were treated with DNase I to remove residual genomic DNA. For miRNA pulldown experiments, RNA was extracted separately from the input lysate and the streptavidin-enriched pulldown fraction using TRIzol reagent. RNA concentration was determined using a Qubit fluorometer or NanoDrop spectrophotometer. RNA integrity was evaluated using an Agilent RNA analysis system when sample yield permitted.
For conventional bulk RNA-seq, libraries were prepared from 200 ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L). Poly(A)-positive RNA was enriched using poly-T oligo-attached magnetic beads, fragmented, reverse-transcribed, adapter-ligated, and PCR-amplified according to the manufacturer’s instructions. For miRNA pulldown RNA-seq, libraries were prepared from RNA recovered from the corresponding input and pulldown fractions using the NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were generated using the same poly(A) enrichment, fragmentation, reverse-transcription, adapter-ligation, and PCR-amplification workflow. Conventional bulk RNA-seq and miRNA pulldown RNA-seq libraries were sequenced using a paired-end 150-bp strategy on an Illumina NovaSeq 6000 or DNBSEQ-T7 platform, as specified for each sample. For small RNA-seq, libraries were prepared from total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300L). Following sequential 3′- and 5′-adapter ligation, reverse transcription, and PCR amplification, library fragments containing 18–40-nt inserts were size-selected. Qualified libraries were sequenced using a single-end 50-bp strategy on an Illumina NovaSeq 6000.

treatment_protocol: For ADAR1-dependent experiments, 32D-LV-H19 cells were transduced with lentiviral vectors expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A. Cells were collected 48 h after transduction. For H19 allele-dependent experiments, primary mouse c-Kit-positive cells were transduced with lentiviral vectors expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant. GFP-positive transduced cells were purified by fluorescence-activated cell sorting before RNA extraction. For inflammatory-stress experiments, H19-A, H19-G, and H19-T mice carrying the Ki67-eGFP reporter were administered polyinosinic acid [poly(I)] at 10 mg/kg. Bone marrow was collected 24 h after treatment, and Ki67-eGFP-negative LT-HSCs were purified by fluorescence-activated cell sorting. For miRNA pulldown experiments, 32D cells were transfected with a biotinylated scrambled-control miRNA mimic, biotinylated unedited wild-type miR-675-3p mimic, or biotinylated edited miR-675-3p mimic. Cells were harvested 48 h after transfection. An aliquot of each cell lysate was retained as the input fraction, and biotinylated miRNA-associated RNA complexes were isolated using streptavidin-coated beads. Steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs were isolated without additional experimental treatment.

value: bone marrow

value: long-term hematopoietic stem cell

value: H19-T editing-resistant allele; Ki67-eGFP reporter

value: poly(I:C), 10 mg/kg, 24 h


title: Q7

description:
Library name: Q7
DAP-seq

value: Klebsiella pneumoniae


title: zinc-adequate (ZA) rep1


title: Q6

description:
Library name: Q6
DAP-seq

value: strain


title: negative control rep4

source_name: negative control

value: negative control


title: negative control rep3


title: Q5

description:
Library name: Q5
DAP-seq

value: genotype

value: WT


title: Poly(I:C)-treated H19-A Ki67-eGFP-negative LT-HSCs, replicate 3

description:
Library name: Sample 24
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: AN_3

value: H19-A control allele; Ki67-eGFP reporter


title: Q4

description:
Library name: Q4
DAP-seq

value: ChIP antibody


title: Pancreatic tumor,KPC,ADT030

city: Birmingham

first: Sujith

last: Sarvesh

state: Alabama

address: 1824 6th Ave S

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: Sample2

data_processing:
Barcoded processing, gene counting, and aggregation were performed using cellranger v10.0 https://www.10xgenomics.com/support/software/cell-ranger/latest
Assembly: GRCm39
Supplementary files format and content: Tab seperated value files and matix files

source_name: Pancreatic Tumor

extract_protocol:
FFPE blocks of the tumor tissues from KPC orthotopic experiments  were used for sc-RNA sequencing, as per the standard protocol used at Admera Health.  After the sequencing, the data were analyzed by demultiplexing and aligned to the mouse reference genome (GRCm39) for gene expression quantification, and processed with Cell Ranger 9.0.1. The count matrices were then analyzed in Seurat (v.5.3.0) R package v.4.5.1. Cells with more than 200 genes and less than 5% mitochondrial content were kept for downstream analysis. After SC Transform analysis, PCA and UMAP were used for dimensionality adjustment and clustering. Differentially expressed genes (DEGs) were identified with FindallMarkers, and clusters were labeled using known markers.
admera Health protocol

value: Pancreatic Tumor

value: KPC


title: negative control rep2

value: intestinal goblet cells


title: Q3

description:
Library name: Q3
DAP-seq


title: Pancreatic tumor,KPC,Vehicle

description: Library name: Sample1

value: Vehicle


title: single cell RNA-seq of Runx3 KO

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample 2

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software ). Briefly, all samples were performed sample de-multiplexing, barcode processing, and single-cell 3' unique molecular identifier (UMI) counting with default parameters. Processed reads were then aligned to GRCh38 genome reference using STAR (2.5.1b). Valid cells were automatically identified based on the UMI number distribution of each cell by using the “barcodeRanks()” function of the DropletUtils tool to remove background beads and the beads that had UMI counts less than the threshold value. Finally, we used PISA to calculate the gene expression of cells and create a gene x cell matrix for each library.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+ T cells

extract_protocol:
The collected tissues were washed by 1× PBS, then quickly frozen and stored in liquid nitrogen. Nuclei extraction was separated by mechanical extraction method. Firstly, put the tissues into 2ml Dounce homogenizer set and thawed in homogenization buffer (containing 20mM Tris pH8.0, 500mM sucrose, 0.1% NP-40, 0.2U/μL RNase inhibitor, 1× protease inhibitor cocktail, 1% bovine serum albumin (BSA), and 0.1mM DTT. Use Dounce pestle A to grind the tissue 10 times, filter with 70μm cell filter, and then grind with Dounce pestle B 10 times, filter with 30um cell filter. Centrifuge at 500 × g for 5 minutes at 4°C to pellet the nuclei, and resuspend in the blocking buffer containing 1% BSA and 0.2U/μL RNase inhibitor in 1× PBS. Centrifuge again at 500 × g for 5 minutes and resuspend with Cell Resuspension Buffer (MGI).
DNBelab C Series High-throughput Single-Cell RNA Library Preparation Set was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 300-500 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the DNBSEQ-T7 sequencing platform with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.

value: CD8+ T cells

value: Runx3 knockout


title: negative control rep1


title: Q2

description:
Library name: Q2
DAP-seq


title: Immune infiltrate, 5555 tumors (Ptgs-/-, NK cell-depleted)

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
Library name: SZ11_03_KO_NK_cell-depleted_S3
10X Genomics

data_processing:
Pre-processing (quality control (QC), alignment and initial filtering for empty droplets) of raw sequencing files was performed using the CellRanger V.3.0.2 (10x Genomics). Output files (either the filtered_feature_bc_matrix.h5 file or the barcodes.tsv, features.tsv and matrix.mtx files) were imported on Partek Flow software (Single cell Toolkit, build version 11.0.24.0325) for analysis. Hashtag demultiplexing was applied on BMDC counts after CLR normalization to specify culture conditions.
Assembly: mm10
Supplementary files format and content: Comma separated meta data files and space-separated count files.

source_name: 5555 Ptgs-/- tumor

extract_protocol:
5555 or CT26 tumors were harvested, cut into small pieces with scissors and incubated in RPMI containing 200U/mL Collagenase IV (Worthington Biochemical) and 0.2mg/mL DNase I (Roche) for 30 min at 37oC. Digested tissue was grinded and filtered through a 70μm cell strainer, washed with RPMI and pelleted. BMDCs cultured in the absence or presence of cancer cells were harvested at day 10. For all experiments, cell suspensions were resuspended in PBS and labelled using LIVE/DEAD Fixable Aqua Dead Cell 405nm staining (Invitrogen) to define cell viability. Samples were rinsed in FACS buffer (PBS containing 1-2% FBS and 0.01% sodium azide) and incubated with the anti-mouse CD45 antibody (clone 30-F11) for 30min at 4oC. Live CD45+ cell suspensions were sorted on a BD FACSAria III with ≥98% purity. Sorted single cells were counted, and ≥90% viability was confirmed through Trypan Blue exclusion.
16-18,000 cells + ~3.5% spike-in (of each 5555 tumor sample) or 25,000 cells (of each CT26 tumor sample) were loaded into a channel of the Chromium Chip B (10x Genomics, PN-1000073). Single cell gel beads-in-emulsion (GEMs) were generated using the Chromium Controller and sequencing libraries prepared using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics), according to the manufacturer’s protocol. For BMDC cultures, 30,000 cells were loaded into a channel of the Chromium Next GEM Chip G (10x Genomics, PN-1000120), and single cell GEMs were generated using the Chromium Controller and Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics) according to the manufacturer’s protocol. Gene expression and TotalSeq-A HTO libraries were produced according to the BioLegend TotalSeq-A protocol and 10x Genomics user guide. For all experiments, libraries were quality checked using the Agilent Bioanalyzer and quantified by qPCR using a KAPA Library Quantification Kit for Illumina Platforms (Roche). Paired-end sequencing was performed on an Illumina NextSeq 500 in High Output mode with an input of 1.4pM (5555) or 1.6pM (CT26), or on an Illumina NovaSeq 6000 with XP loading and inputs of 0.9 (GEx library) and 1.8pM (HTO library).

value: 5555 Ptgs-/- tumor

value: Immune cells

tag: strain

value: NK cell depletion (anti-NK1.1 clone PK136, anti-Asialo GM-1)


title: Immune infiltrate, CT26 tumors

description:
Library name: SZ13_01_10X_vehicle
10X Genomics

source_name: CT26 tumor

value: CT26 tumor

value: BALB/c


title: Q19

description:
Library name: Q19
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Q20

description:
Library name: Q20
DAP-seq

value: genotype


title: Immune infiltrate, 5555 tumors (Ptgs-/-)

description:
Library name: SZ11_02_KO_S2
10X Genomics


title: Q18

description:
Library name: Q18
DAP-seq

value: WT


title: Immune infiltrate, 5555 tumors (Ptgs+/+)

description:
Library name: SZ11_01_WT_S1
10X Genomics

source_name: 5555 Ptgs+/+ tumor

value: 5555 Ptgs+/+ tumor


title: Q16

description:
Library name: Q16
DAP-seq

value: ChIP antibody


title: 12_SNAT2_cKO_S10_L001_R1_001.fastq

city: haifa

first: Herman

last: Wolosker

address: 1 Efron St

department: Biochemistry

institute: Technion-Israel Institute of Technology

description:
Library name: 12_SNAT2_cKO_S10_L001_R1_001.fastq
Slc38a2-cKO

data_processing:
Quality control was assessed using Fastqc (v0.12.1). Reads were trimmed for adapters, minimum quality Phred score of 20 and minimum length of 35 using CUTADAPT (v4.4).
Single reads (100 bp) were aligned to Mus musculus (GRCm39) reference genome and annotation file using STAR (v2.7.10b) with mismatch ratio allowed < 0.2, the minimum and maximum intron sizes were set to 21 and 1,000,000, respectively. The number of reads per gene was counted using STAR “--quantMode GeneCounts” (v2.7.10b) with ‘reverse’ mode.
Normalization and differential expression analyses were conducted using DESeq2 R package (v1.41.8). The threshold for significantly differentially expressed genes is determined by two factors: adjusted p-value ≤ 0.05 and the ‘base-mean independent filtering’ threshold, which is calculated by the DESeq2 algorithm for each comparison. FDR was calculated using the default approach of DESeq2, Benjamini-Hochberg.
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: Excel file with differential gene expression comparisons including log fold-change and FDR values.

source_name: hippocampus

extract_protocol:
Total RNA was extracted from 9 tissue samples using the RNeasy mini kit (Qiagen, cat no. 74106). 600 ul of RLT buffer was added to each sample and the samples were disrupted and homogenized using the Polytron PT3000 Homogenizer (Kinematica). After homogenization, samples were centrifuged for 3 min at 13000g and the supernatant was transferred to a new tube for automated extraction using the QIAcube Connect (Qiagen). The RINe value of all samples was in the range of 9.7-9.9, indicating very high quality.
RNA-seq libraries were constructed simultaneously using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7760), according to the manufacturer’s protocol.

treatment_protocol: Hippocampi were dissected, flash-frozen in liquid nitrogen and stored at −80°C until further analysis

value: hippocampus

value: Regular chow diet


title: Q17

description:
Library name: Q17
DAP-seq


title: Q15

description:
Library name: Q15
DAP-seq


title: 11_WT_S9_L001_R1_001.fastq

description:
Library name: 11_WT_S9_L001_R1_001.fastq
WT


title: 10_WT_S8

description:
Library name: 10_WT_S8
WT


title: Q14

description:
Library name: Q14
DAP-seq


title: 9_SNAT2_cKO_S7

description:
Library name: 9_SNAT2_cKO_S7
Slc38a2-cKO


title: Q13

description:
Library name: Q13
DAP-seq


title: 7_SNAT2_cKO_S5

description:
Library name: 7_SNAT2_cKO_S5
Slc38a2-cKO


title: Q12

description:
Library name: Q12
DAP-seq


title: Q11

description:
Library name: Q11
DAP-seq


title: 6_WT_S4

description:
Library name: 6_WT_S4
WT


title: 8_WT_S6

description:
Library name: 8_WT_S6
WT


title: 3_SNAT2_cKO_S2

description:
Library name: 3_SNAT2_cKO_S2
Slc38a2-cKO


title: P9

description:
Library name: P9
DAP-seq


title: P8

description:
Library name: P8
DAP-seq


title: 4_SNAT2_cKO_S3

description:
Library name: 4_SNAT2_cKO_S3
Slc38a2-cKO


title: P7

description:
Library name: P7
DAP-seq


title: 2_WT_S1

description:
Library name: 2_WT_S1
WT


title: M15H1_S5

description:
Library name: M15H1_S5
Ser/Gly Restricted diet (RD)

value: 4 weeks

value: Ser/Gly Restricted diet (RD)


title: P6

description:
Library name: P6
DAP-seq


title: P5

description:
Library name: P5
DAP-seq


title: WD844

type: genomic

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: genomic DNA was hybridized to Agilent 244K or 1M oligonucleotide arrays per manufacturer's instructions in the presence of a DNA reference set (Human Genomic DNA from blood (buffy coat); Roche Applied Science)

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C at 3 microns per pixel resolution in two-color mode. Images were extracted using Agilent Feature Extraction software version 10.2.1.3.

data_processing:
Array comparative genomic hybridization (aCGH) was performed using Agilent 244K or 1M arrays and analyzed using the RAE pipeline as previously reported.(14, 28).
progV2aCGHMatrixTable_260619_v2__final.csv: Log2 ratio of Cy5 (sample) to Cy3 (reference) signal intensities, background-corrected and dye-normalized by Agilent Feature Extraction software.

source_name: Human Genomic DNA, blood (buffy coat), Roche Applied Science

label_protocol: per Agilent protocols

growth_protocol: not applicable

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols

treatment_protocol: not applicable

value: blood (buffy coat)

source_name: surgical specimen

tag: tumor class

value: Well-differentiated

value: retroperitoneal


title: WD842

value: Dedifferentiated


title: M14H1_S4

description:
Library name: M14H1_S4
Ser/Gly Restricted diet (RD)


title: WD828


title: M13H1_S3

description:
Library name: M13H1_S3
Ser/Gly Restricted diet (RD)


title: P4

description:
Library name: P4
DAP-seq

source_name: Klebsiella pneumoniae


title: WD824


title: WD821_791


title: M12H1_S2

description:
Library name: M12H1_S2
Ser/Gly Restricted diet (RD)


title: P3

description:
Library name: P3
DAP-seq


title: WD820_790


title: P20

description:
Library name: P20
DAP-seq


title: WD810


title: M11H1_S1

description:
Library name: M11H1_S1
Ser/Gly Restricted diet (RD)


title: WD804


title: P2

description:
Library name: P2
DAP-seq


title: M5H1_S10

description:
Library name: M5H1_S10
Control diet (CD)

value: Control diet (CD)


title: WD806


title: P19

description:
Library name: P19
DAP-seq


title: WD802


title: WD803


title: M4H1_S9

description:
Library name: M4H1_S9
Control diet (CD)


title: WD794


title: P18

description:
Library name: P18
DAP-seq


title: WD72


title: M3H1_S8

description:
Library name: M3H1_S8
Control diet (CD)


title: WD722


title: WD691


title: P17

description:
Library name: P17
DAP-seq


title: M2H1_S7

description:
Library name: M2H1_S7
Control diet (CD)


title: WD418


title: P16

description:
Library name: P16
DAP-seq


title: M1H1_S6

description:
Library name: M1H1_S6
Control diet (CD)


title: WD419


title: P15

description:
Library name: P15
DAP-seq


title: WD199


title: WD196


title: CHX_Efruxifermin_5

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

description:
Library name: NGS-78-177
Column name in genesRPMTable.xlsx: 347_Efruxi

data_processing:
Raw reads were quality controlled using FastQC. Adapter sequences were trimmed using Cutadapt with a minimum read length of 17 bp and a quality cutoff of 30 (Phred score, 99.9% base call accuracy). Quality-filtered reads were mapped to the Mus musculus reference genome (GRCm39 p1) using HISAT2. Gene-level read counts were quantified using HTSeq-count. Gene expression levels were normalized as Reads Per Million (RPM).
Assembly: GRCm39 p1
Supplementary files format and content: Tab-delimited Excel file (genesRPMTable.xlsx) containing gene expression values (RPM - Reads Per Million) for all samples. Rows represent genes with Ensembl gene IDs, gene symbols, and descriptions. Columns represent individual samples.

source_name: Inguinal adipose tissue

growth_protocol: Mice (WT, C57BL/6JRj) were acclimatized to thermoneutral conditions (29°C) for 14 days prior to tumor cell injection. Generally, mice were housed at thermoneutrality with ad libitum access to food and water and a 12 h light 12 h dark cycle.

extract_protocol:
Mouse tissues were homogenized in Trizol reagent (1 ml per 50 mg) and phase separation was performed by the addition of 0.2 ml chloroform per ml of Trizol reagent. The aequous phase was further processed using the Relia Prep RNA Tissue Miniprep reagent. The aequous phase was further processed using the Relia Prep RNA Tissue Miniprep System.
Total RNA was extracted from inguinal white adipose tissue using Trizol reagent followed by cleanup with the ReliaPrep RNA Tissue Miniprep System (Promega). RNA-seq libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina according to the manufacturer's instructions. This kit generates Illumina-compatible libraries for sequencing of the last exon with a 3' bias.

treatment_protocol: Tumors were induced by intramuscular injection of 1x10^6 CHX 207 fibrosarcoma cells into the right gastrocnemius. Tumor bearing mice were treated with either control AAV (2x10^10 vgc; i.v.; 9 days pre tumor cell injection), FGF21 AAV (2x10^10 vgc; i.v.; 9 days pre tumor cell injection) or Efruxifermin (2 mg/kg,; i.p.; start 9 days pre tumor cell injection, every 3-4 days for a total of 6 injections). Healthy controls were treated with control AAV (2x10^10 vgs; i.v.) and PBS (i.p.). Mice were sacrificed 14 days post tumor cell injection.

value: Inguinal adipose tissue

value: Whole adipose tissue

tag: time

value: Termination day 14 post tumor cell injection

value: Thermoneutrality adapted, CHX Tumor, Efruxifermin


title: WD1568


title: CHX_Efruxifermin_4

description:
Library name: NGS-78-175
Column name in genesRPMTable.xlsx: 346_Efruxi


title: P14

description:
Library name: P14
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype


title: WD1362


title: WD1349


title: WD1344


title: P12

description:
Library name: P12
DAP-seq

value: WT

value: ChIP antibody


title: WD1342


title: WD1352


title: CHX_Efruxifermin_3

description:
Library name: NGS-78-182
Column name in genesRPMTable.xlsx: 345_Efruxi


title: P13

description:
Library name: P13
DAP-seq


title: CHX_Efruxifermin_2

description:
Library name: NGS-78-178
Column name in genesRPMTable.xlsx: 342_Efruxi


title: WD1340


title: P11

description:
Library name: P11
DAP-seq


title: WD1338


title: CHX_Efruxifermin_1

description:
Library name: NGS-78-186
Column name in genesRPMTable.xlsx: 340_Efruxi


title: WD1336


title: WD1309


title: P10

description:
Library name: P10
DAP-seq


title: CHX_FGF21AAV_5

description:
Library name: NGS-78-179
Column name in genesRPMTable.xlsx: 338_AAV

value: Thermoneutrality adapted, CHX Tumor, FGF21 AAV


title: P1

description:
Library name: P1
DAP-seq


title: WD1308


title: WD1306


title: CHX_FGF21AAV_4

description:
Library name: NGS-78-174
Column name in genesRPMTable.xlsx: 337_AAV


title: O9

description:
Library name: O9
DAP-seq


title: WD1297


title: CHX_FGF21AAV_3

description:
Library name: NGS-78-172
Column name in genesRPMTable.xlsx: 336_AAV


title: WD1296


title: O8

description:
Library name: O8
DAP-seq


title: WD1243


title: WD1305


title: CHX_FGF21AAV_2

description:
Library name: NGS-78-184
Column name in genesRPMTable.xlsx: 334_AAV


title: WD1226


title: WD1219


title: O7

description:
Library name: O7
DAP-seq


title: WD1216


title: CHX_FGF21AAV_1

description:
Library name: NGS-78-171
Column name in genesRPMTable.xlsx: 333_AAV


title: O6

description:
Library name: O6
DAP-seq


title: WD1218


title: WD1205


title: O20

description:
Library name: O20
DAP-seq


title: CHX_untreated_5

description:
Library name: NGS-78-173
Column name in genesRPMTable.xlsx: 329_CHX

value: Thermoneutrality adapted, CHX Tumor, Control AAV


title: WD1158


title: WD1134


title: O2

description:
Library name: O2
DAP-seq


title: CHX_untreated_4

description:
Library name: NGS-78-170
Column name in genesRPMTable.xlsx: 328_CHX


title: CHX_untreated_3

description:
Library name: NGS-78-176
Column name in genesRPMTable.xlsx: 326_CHX


title: WD1128


title: TK23

status: Public on Aug 05 2026

city: Boston

first: Jason

last: Williams

state: MA

address: 77 Ave Louis Pasteur, Building HIM Room 660

department: Dermatology

institute: Brigham and Women's Hospital

description:
Library name: TK23_CD8_TumorAdjSkin_CD103-CD69-
3 mice pooled, day 42 post TAM

data_processing:
Sequencing data was processed and analyzed using Partek software.  Alignment was performed by the STAR alignment method.  Raw read counts were processed by TMM normalization.  Differentially expressed genes were determined by normalization to spleen CD8 samples with a cutoff fold-change > 2 and adjusted p-value <0.05.
Assembly: GRCm39
Supplementary files format and content: Gene counts

source_name: Tumor Adj Skin

extract_protocol:
Autochthonous BPO tumors were digested with collagenase IV, DNase IV, and hyaluronidase V for 30 min at 37C. Tumors were mashed through a cell strainer and Ficolled to remove dead cells. Single cell suspensions were stained with antibodies and cell sorted.
Library preparation and RNA sequencing was performed by the Dana-Farber Molecular Biology Core Facilities using Takara SmartSeq v4 reagents for low input mRNASeq. Samples with an RNA quality (RIN) score >7 were used for sequencing.  Full-length cDNA was fragmented to an average size of 200 bp, and sequencing libraries were prepared from 2 ng of sheared cDNA. Double-stranded DNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Uniquely dual-indexed libraries were pooled in equimolar amounts, assessed for cluster efficiency and pool balance with shallow sequencing on an Illumina MiSeq

value: Tumor Adj Skin

value: CD8+ T cell


title: WD1121

value: blood (buffy coat)

value: Well-differentiated


title: O19

description:
Library name: O19
DAP-seq


title: CHX_untreated_2

description:
Library name: NGS-78-180
Column name in genesRPMTable.xlsx: 325_CHX


title: WD1119

value: retroperitoneal


title: O18

description:
Library name: O18
DAP-seq


title: WD1118


title: WD1117


title: O17

description:
Library name: O17
DAP-seq


title: WD1124


title: CHX_untreated_1

description:
Library name: NGS-78-183
Column name in genesRPMTable.xlsx: 324_CHX


title: Healthy_control_4

description:
Library name: NGS-78-185
Column name in genesRPMTable.xlsx: 319_healthy

value: Thermoneutrality adapted, Tumor-free, Control AAV


title: WD1115


title: WD1111


title: WD1086


title: Healthy_control_3

description:
Library name: NGS-78-187
Column name in genesRPMTable.xlsx: 318_healthy

value: Inguinal adipose tissue


title: O16

description:
Library name: O16
DAP-seq


title: WD1084


title: WD1083


title: O15

description:
Library name: O15
DAP-seq


title: Healthy_control_2

description:
Library name: NGS-78-188
Column name in genesRPMTable.xlsx: 317_healthy

value: Whole adipose tissue


title: WD1082


title: O14

description:
Library name: O14
DAP-seq


title: WD1068


title: WD1070


title: O13

description:
Library name: O13
DAP-seq


title: WD1066


title: WD1053


title: Tree peony buds, H3K4me3, Chilling, 21, biol rep 2 (INPUT)

city: Qingdao

first: Yuxi

last: Zhang

address: Changcheng Road 700

institute: Qingdao Agricultural University

description: Library name: Tree peony buds_21_biol rep 2, INPUT

data_processing:
The raw image data files obtained from Illumina NovaSeq are converted into raw sequencing reads through base calling.
ChlP-seg reads filtering with Trimmomatic (v0.36), the filtered data underwent quality control processing using fastqc (v0.11.5).
ChlP-seg reads were aligned to the Paeonia ostii genome using Bwa (v0.7.15).
After obtaining information on the valid reads aligned to the genome, MACS (v2.1.1) was employed to analyze peaks information genome-wide with the significance cut-off q-value <0.05.
Log2[ratio] bigwig coverage files relative to the input were generated using the bamCompare function of deepTools (v3.5.6). The bigwig files were visualized as H3K4me3 signals using the Integrative Genomics Viewer (v2.18.2) and deepTools.
Assembly: CNA0050666 (Paeoniaostii_Fengdan.fa)
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Paeonia suffruticosa

source_name: buds

growth_protocol: Four-year-old Paeonia suffruticosa 'Luhehong' plants were subjected tochilling treatments at 0-4℃ for 0, 14, and 21 days. Scales were removed from buds collected at 0, 14, and 21 days.

extract_protocol:
Samples were washed twice with cold PBS buffer and subsequently cross-linked with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched by the addition of glycine to a final concentration of 125 mmol/L.
Immunoprecipitated DNA was utilized to construct sequencing libraries in accordance with the protocol provided by the INEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing (NOVA-5143-02, Bioo Scientific). The sequencing was performed on the Illumina NovaSeq 6000 using the PE150 method.

value: buds

tag: chip antibody

value: Chilling

value: 21 days


title: WD0611


title: Tree peony buds, H3K4me3, Chilling, 21, biol rep 1 (INPUT)

description: Library name: Tree peony buds_21_biol rep 1, INPUT


title: O12

description:
Library name: O12
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: DD841

value: Dedifferentiated


title: O11

description:
Library name: O11
DAP-seq

value: genotype

value: WT

value: ChIP antibody


title: DD8379


title: Tree peony buds, H3K4me3, Chilling, 21, biol rep 2 (ChIP)

description: Library name: Tree peony buds_21_biol rep 2, ChIP

value: H3K4me3 (Abcam, #ab8580)


title: O10

description:
Library name: O10
DAP-seq


title: Col0-BL-AsA

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

description: Library name: Sample2

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw

organism: Arabidopsis thaliana

source_name: true leaf

extract_protocol:
The chloroplasts were embedded in 0.5% low-melting-point agarose (Promega) and lysed in 1% sarkosyl, 0.45 M EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), and 2 mg/mL proteinase K at 48°C for 16 h with shaking. The agarose plugs were washed in TE buffer six times at 37°C, with the first two washes containing 1 mM PMSF. Cut agarose plug into 12 pieces and incubated in 1 ml TE with 10 μg/ml RNase A at 37°C overnight. The agarose pieces were washed five times with 1 ml TE buffer at 37°C for 6 min, then stored in plug storage solution (0.05 M EDTA pH 8.0, 60% glycerol) at -20°C until all samples were ready for the next step.
The DNA library was constructed with Scale ssDNA-seq Lib Prep Kit for Illumina V2 (ABclonal, RK20228). Five agarose pieces (~30 mg) were washed three times with 200 μl 1× CutSmart buffer (NEB) at 37°C for 6 min. The spike-in was performed by incubating the agarose pieces with 15 U I-CeuI (NEB) in 150 μl 1× CutSmart buffer at 37°C for 12 h. After digestion, the agarose pieces were washed three times with 500 μl TE buffer at 37°C for 6 min, followed by twice washes with 200 μl Low EDTA TE (ABclonal) at 37°C for 6 min. The agarose pieces were incubated in 80 μl T7 Tailing & Ligation buffer (ABclonal) at 37°C for 12 h. Then, heated the agarose pieces at 98°C for 2 min. The DNA in the agarose was recovered using a DNA purification kit (Magen, Catalog No D2111-02) and eluted with Low EDTA TE. The DNA was then sonicated to ~250 bp using Focused-ultrasonicator (Covaris S220). To finish the library preparation, the subsequent steps were performed according to the manufacturer's protocol exactly.

value: true leaf

tag: ecotype

value: wildtype

value: Blue light and 0.5 mM ascorbic acid


title: DD822/792

value: blood (buffy coat)

value: retroperitoneal


title: DD807


title: Tree peony buds, H3K4me3, Chilling, 21, biol rep 1 (ChIP)

description: Library name: Tree peony buds_21_biol rep 1, ChIP


title: DD795


title: O1

description:
Library name: O1
DAP-seq


title: DD793


title: Tree peony buds, H3K4me3, Chilling, 14, biol rep 2 (INPUT)

description: Library name: Tree peony buds_14_biol rep 2, INPUT

value: 14 days


title: DD789


title: DD788


title: N9

description:
Library name: N9
DAP-seq


title: Tree peony buds, H3K4me3, Chilling, 14, biol rep 1 (INPUT)

description: Library name: Tree peony buds_14_biol rep 1, INPUT


title: DD787


title: N8

description:
Library name: N8
DAP-seq


title: DD786


title: Tree peony buds, H3K4me3, Chilling, 14, biol rep 2 (ChIP)

description: Library name: Tree peony buds_14_biol rep 2, ChIP


title: DD506


title: DD471


title: Tree peony buds, H3K4me3, Chilling, 14, biol rep 1 (ChIP)

description: Library name: Tree peony buds_14_biol rep 1, ChIP


title: N7

description:
Library name: N7
DAP-seq


title: DD216


title: N6

description:
Library name: N6
DAP-seq


title: DD1405


title: DD1346


title: Tree peony buds, H3K4me3, Chilling, 0, biol rep 2 (INPUT)

description: Library name: Tree peony buds_0_biol rep 2, INPUT

value: 0 days


title: N5

description:
Library name: N5
DAP-seq


title: Tree peony buds, H3K4me3, Chilling, 0, biol rep 1 (INPUT)

description: Library name: Tree peony buds_0_biol rep 1, INPUT

value: buds


title: DD1299


title: DD1304


title: N4

description:
Library name: N4
DAP-seq


title: DD1278


title: Tree peony buds, H3K4me3, Chilling, 0, biol rep 2 (ChIP)

description: Library name: Tree peony buds_0_biol rep 2, ChIP

value: Chilling


title: N3

description:
Library name: N3
DAP-seq


title: DD1295


title: DD1244


title: Tree peony buds, H3K4me3, Chilling, 0, biol rep 1 (ChIP)

description: Library name: Tree peony buds_0_biol rep 1, ChIP


title: DD1230


title: N20

description:
Library name: N20
DAP-seq


title: DD1229


title: FaWRKY71-RNAi_3

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

description: Library name: Sample_3_3

data_processing:
RNA-seq library construction and sequencing were performed by Beijing Novogene Technology Co., Ltd. (Beijing, China) using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s protocol.
Assembly: Fragaria vesca Whole Genome v4.0.a1
Supplementary files format and content:
tab-delimited text file includes raw counts for each sample.
the identifiers can be searched at:
https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a1

organism: Fragaria x ananassa

source_name: fruit receptacle

growth_protocol: Plants grown at 25 °C, 10 000 lux and 80% humidity

extract_protocol:
Total RNA was isolated and purified from three independent biological replicates using an automated extraction system Maxwell® 16 Lev Plant RSC Instrument (manufactured by Promega Corporation, Wisconsin, USA) using a Maxwell® RSC RNA FFPE kit (AS1440, Promega, Wisconsin, USA). The process was conducted according to the manufacturer’s instructions.
Illumina’s TruSeq Stranded mRNA Library Prep Kit was used to prepare the libraries following the manufacturer’s instructions. Briefly, each sample was enriched in mRNA by selection 3’ poly(A) tails using poly(T) magnetic beads. Captured mRNAs were then converted into cDNA, and sequencing adaptors were added to their ends to make the molecules ready for sequencing. Samples were dual-indexed for post-sequencing demultiplexing. The fragment size distribution and concentration of the libraries were checked in an Agilent 2100 Bioanalyzer using the Agilent DNA 1000 kit. These were sequenced into a HiSeq-4000 Illumina platform as 2x100b paired-end sequences.

treatment_protocol: Non-treated plants

value: fruit receptacle

tag: genotype background

value: Fragaria x ananassa cv Chandler

value: non-treated plants


title: DD1227

value: Dedifferentiated


title: OVCAR-8, H3K27me3, rep1

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: High grade ovarian serous adenocarcinoma


title: DD1225


title: DD1223


title: Col0-BL

description: Library name: Sample1

value: Blue light


title: DD1196


title: DD1220


title: N19

description:
Library name: N19
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype

value: WT

value: ChIP antibody


title: N18

description:
Library name: N18
DAP-seq


title: N2

description:
Library name: N2
DAP-seq


title: FaWRKY71-RNAi_1

description: Library name: Sample_3_1


title: DD1195

value: blood (buffy coat)


title: Control_3_1

description: Library name: Cont_2_3

value: Control


title: FaWRKY71-RNAi_2

description: Library name: Sample_3_2


title: DD1194

value: retroperitoneal


title: N17

description:
Library name: N17
DAP-seq


title: DD1193


title: Control_2_1

description: Library name: Cont_2_2


title: DD1159


title: DD1192


title: Control_1_1

description: Library name: Cont_2_1


title: N16

description:
Library name: N16
DAP-seq


title: DD1148


title: Healthy_control_1

description:
Library name: NGS-78-181
Column name in genesRPMTable.xlsx: 316_healthy

value: Inguinal adipose tissue

value: Whole adipose tissue

value: Termination day 14 post tumor cell injection

value: Thermoneutrality adapted, Tumor-free, Control AAV


title: N15

description:
Library name: N15
DAP-seq


title: cCEO_N2_RNA-Seq

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

institute: TUD Dresden University of Technology

description: Library name: 111678

data_processing:
sequence data files were created with bclconvert 4.4.6
RNA-seq libraries were mapped and de-duplicated using STAR with default settings and each libraries was aligned to the human (hg38) and chimpanzee (panTro6) reference separately. Gene-level read counts were generated using STAR (--quantMode GeneCounts) during alignment.
Assembly: hg38/panTro6
Supplementary files format and content: C_count_table_hg38.tsv.gz: Raw gene counts for chimpanzee RNA-seq samples mapped to hg38
Supplementary files format and content: C_count_table_panTro6.tsv.gz: Raw gene counts for chimpanzee RNA-seq samples mapped to panTro6

organism: Pan troglodytes

source_name: cerebral organoid

growth_protocol: iPSC line grown under standard conditions (5 % CO2, 37 °C) on Matrigel-coated plates in mTeSR1. Cerebral organoids were generated as whole spheres using the STEMdiff Cerebral Organoid Kit or equivalent self-made medium based on previous publications with small modifications as described in detail (Lancaster & Knoblich, 2014; Giandomenico, Sutcliffe & Lancaster, 2021). Briefly, 9,000 cells were seeded into 96-well Ultra-Low Attachment plates and cultured in mTeSR1 containing 10 µM Y-27632 rho kinase inhibitor. Plates were spun for 3 min at 300x g to settle cells. After 48 hours, the medium was changed to mTeSR1 without Y-27632 rho kinase inhibitor (organoid formation medium). On day 4, the now-formed embryoid bodies (EBs) were changed to neural induction medium. EBs were embedded in Matrigel on day 8, transferred to differentiation medium containing B27 supplement without vitamin A (expansion medium), and henceforth cultured on an orbital shaker. Starting on day 14, young organoids were changed to, and then maintained in, differentiation medium containing B27 supplement with vitamin A (maturation medium), changed every 2–3 days until collection for experiments. All cerebral organoids were collected for experiments on w8 ± 3 days.

extract_protocol:
RNA extraction was performed as per the manufacturer’s instructions using the Zymo QuickRNA FFPE MiniPrep Kit
libraries were prepared using the SmartSeq 2 protocol, modified from Picelli et al. 2013. Isolated total RNA from 10,000 cells was denatured for 3 min at 72 °C in 4 μL hypotonic buffer (0.2 % Triton X-100) in the presence of 2.4 mM dNTPs, 240 nM dT-primer and 4 U RNase Inhibitor (NEB). Reverse transcription was performed at 42 °C for 90 min after filling up to 10 µL with RT buffer mix for a final concentration of 1x Superscript II buffer, 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer, 9 U RNase inhibitor and 90 U Superscript II Reverse Transcriptase. The reverse transcriptase was inactivated at 70 °C for 15 min. For subsequent PCR amplification of the cDNA, the optimal PCR cycle number was determined with an aliquot of 1 μL unpurified cDNA in a 10 μL qPCR containing 1x KAPA HiFi Hotstart Readymix, 1x SYBR Green I and 0.2 μM UP primer. The determined cycle number was then used to amplify the residual 9 μL cDNA using 1x KAPA HiFi HotStart Readymix and 250 nM UP-primer under the following cycling conditions: initial denaturation at 98 °C for 3 min, 12–17 cycles [98 °C 20 sec, 67 °C 15 sec, 72 °C 6 min] and final elongation at 72 °C for 5 min. The amplified cDNA was purified using 0.6x Sera-Mag SpeedBeads and resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. cDNA quality and concentration were determined using the FragmentAnalyzer NGS 1-6000bp Kit.  For library preparation, 2 µL amplified cDNA was tagmented in 1x Tagmentation Buffer using 0.8 µL bead-linked transposome (Illumina) at 55 °C for 15 min in a total volume of 4 µL. The reaction was stopped by the addition of 1 µL 0.1 % SDS (37 °C, 15 min), beads were bound to a magnet and the supernatant was removed. Beads were then resuspended in 14 µL indexing PCR Mix containing 1x KAPA Hifi HotStart Ready Mix and 700 nM unique dual indexing primers (i5 and i7), and subjected to a PCR (72 °C 3 min, 98°C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72 °C 5 min). Libraries were purified with 0.9x volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6x and 0.9x. Repurification with a final 0.9x bead purification was performed if needed. Sequencing was performed after quantification using the FragmentAnalyzer NGS 1-6000bp Kit (Agilent) on a NovaSeq S4 v1.5 200 cycles flow cell (Illumina) to a sequencing depth of at least 50 million 100 bp paired-end reads per library.

value: cerebral organoid

value: SandraA

value: BCL11B+ neuron


title: N14

city: Hongkong

first: Xin

last: Deng

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

institute: City University of Hong Kong

description:
Library name: N14
DAP-seq

data_processing:
Quality-filtered paired reads were mapped to the reference genome, and gene-level quantification was performed using featureCounts (Subread v2.0.1) against annotated features. The resulting count matrix was analyzed using DESeq2 (v1.40.2).
Assembly: Genome assembly ASM585424v1
Supplementary files format and content: The bed file for each DAP-seq displayed the TF binding sites. The counts txt files contained the gene expression counts for each RNA-seq.

extract_protocol:
Total RNA was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen, # Gdp430) and depleted of rRNA using NEBNext® rRNA Depletion Kit (Bacteria) (NEB, #E7850).
Libraries were constructed with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, #E7770L) and sequenced on the Illumina Xten platform.


title: DD1131

value: Dedifferentiated


title: DD1129


title: cCEO_bIP2_RNA-Seq

description: Library name: 111677

value: basal intermediate progenitor cell


title: DD1132


title: N13

description:
Library name: N13
DAP-seq

value: Klebsiella pneumoniae


title: cCeO_bRG2_RNA-Seq

description: Library name: 111676

value: basal radial glia


title: DD112


title: DD1087


title: N12

description:
Library name: N12
DAP-seq

value: strain

value: genotype


title: DD1085


title: cCeO_aRG2_RNA-Seq

description: Library name: 111675

value: apical radial glia


title: N11

description:
Library name: N11
DAP-seq

value: WT

value: ChIP antibody


title: DD1081

value: blood (buffy coat)

value: retroperitoneal


title: DD1080


title: DD1077


title: PBMC, XJY-HC

city: Hangzhou

first: Jinyan

last: Xie

address: No.866 Yuhangtang Road

institute: zhejiang university

description:
Library name: Sample6
10X Genomics

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. Then the feature-barcode matrices were obtained by aligning reads to the mouse genome using CellRanger v7.1.0 (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using LeucoSep tubes prefilled with Ficoll-Paque Plus, following the manufacturer’s instructions. Samples were centrifuged at 700g for 20 minutes, and PBMCs were collected from the upper layer of the interphase. The cells were then resuspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse any remaining erythrocytes. Following red blood cell lysis, PBMCs were washed twice to remove any ambient RNA and resuspended in 1X PBS (calcium- and magnesium-free) containing 0.04% bovine serum albumin (BSA). The cell suspensions were passed through a 30-µm Flowmi Cell Strainer to ensure a single-cell suspension. Only cells with greater than 90% viability were selected for further processing and kept on ice prior to fixation and single-cell RNA analysis.
In brief, the scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA). Briefly, cells were concentrated to 1000 cells/uL and approximately 10,000 cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 5,000 single-cells for each sample. After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Qsep100 (Bioptic). All libraries were sequenced by NovaSeq 6000 (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: PBMC


title: N1

description:
Library name: N1
DAP-seq


title: N10

description:
Library name: N10
DAP-seq


title: cCEO_bIP1_RNA-Seq

description: Library name: 109459


title: PBMC, WDH-HC

description:
Library name: Sample5
10X Genomics


title: cCEO_N1_RNA-Seq

description: Library name: 109460


title: DD1076


title: PBMC, GXL-HC

description:
Library name: Sample4
10X Genomics


title: M9

description:
Library name: M9
DAP-seq


title: DD1075


title: cCeO_bRG1_RNA-Seq

description: Library name: 109458


title: cCeO_aRG1_RNA-Seq

description: Library name: 109457


title: M8

description:
Library name: M8
DAP-seq


title: PBMC, ymx-sepsis

description:
Library name: Sample3
10X Genomics


title: cCeO_N2_ATAC-seq

description:
Library name: 110601
GEO_chimp_ATAC_counts.tsv.gz
cCeO_N_consensusPeak.narrowPeak.gz

data_processing:
sequence data files were created with bcl2fastq2 v2.20.0
ATAC-seq libraries were mapped and processed using the ENCODE pipeline (Lee et al. 2016) with default settings. This includes that creating narrowPeak files with MACS2, conversion of bed files to bw files and count tables
consensusPeak.narrowPeak files represent IDR-filtered high-confidence ATAC-seq peaks representing reproducible chromatin accessibility regions across biological replicates.
Assembly: panTro6
Supplementary files format and content: bigWig: Normalized ATAC-seq signal tracks for genome browser visualization.
Supplementary files format and content: narrowPeak: Called accessible chromatin peaks with genomic coordinates and peak statistics.
Supplementary files format and content: GEO_chimp_ATAC_counts.tsv.gz: Raw counts per peak across samples with genomic/gene annotations and liftover to human (hg38) and gorilla (gorgor6)

extract_protocol:
ATAC-seq was performed as previously described with minor alterations to the protocol (Corces et al. 2017). Briefly, sorted cells are pelleted at 500x g and 4 °C for 5 min. All supernatant was aspirated, cells were re-suspended in 50 µL ice-cold lysis buffer by pipetting up-and-down three times and incubated on ice for 3 min. Lysis was washed out with 1 mL ice-cold wash buffer, and the tubes were inverted to mix. Cells were again pelleted at 500x g and 4 °C for 10 min. Supernatant was fully aspirated and cells re-suspended in 50 µL transposition mix containing 100 mM transposase. Reactions were incubated at 37 °C and 1,000 rpm in a thermoshaker for 2 hours and then quenched by the addition of 40 mM EDTA. Reactions were pelleted at 500x g for 5 min, re-suspended in 200 µL reverse-crosslink solution and incubated O/N at 65 °C and 1,000 rpm in a thermoshaker as previously reported for ATAC-seq on fixed cells (Chen et al. 2020). The next day, the original protocol was continued, and reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit.
libraries were amplified with determination of amplification cycles by qPCR as described (Corces et al. 2017) and unique adapter combinations (i5 and i7), and final PCR reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit. Final libraries were size selected using SPRIselect Beads at 0.5x and 1.3x ratios, to retain fragments of 150–1,000 bp.

treatment_protocol: ATAC-seq was performed as previously described with minor alterations to the protocol95. Briefly, sorted cells are pelleted at 500x g and 4 °C for 5 min. All supernatant was aspirated, cells were re-suspended in 50 µL ice-cold lysis buffer by pipetting up-and-down three times and incubated on ice for 3 min. Lysis was washed out with 1 mL ice-cold wash buffer, and the tubes were inverted to mix. Cells were again pelleted at 500x g and 4 °C for 10 min. Supernatant was fully aspirated and cells re-suspended in 50 µL transposition mix containing 100 mM transposase. Reactions were incubated at 37 °C and 1,000 rpm in a thermoshaker for 2 hours and then quenched by the addition of 40 mM EDTA. Reactions were pelleted at 500x g for 5 min, re-suspended in 200 µL reverse-crosslink solution and incubated O/N at 65 °C and 1,000 rpm in a thermoshaker as previously reported for ATAC-seq on fixed cells96. The next day, the original protocol95 was continued, and reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit, libraries were amplified with determination of amplification cycles by qPCR as described95 and unique adapter combinations (i5 and i7), and final PCR reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit. Final libraries were size selected using SPRIselect Beads at 0.5x and 1.3x ratios, to retain fragments of 150–1,000 bp.


title: PBMC, WHF-sepsis

description:
Library name: Sample2
10X Genomics


title: DD1074


title: M7

description:
Library name: M7
DAP-seq


title: DD1073


title: PBMC, CZJ-sepsis

description:
Library name: Sample1
10X Genomics


title: cCeO_bIP2_ATAC-seq

description:
Library name: 110600
GEO_chimp_ATAC_counts.tsv.gz
cCeO_bIP_consensusPeak.narrowPeak.gz


title: DD1072


title: M6

description:
Library name: M6
DAP-seq


title: HepG2, Eliglustat30, rep3

city: Milan

first: Italia

last: Bongarzone

state: Milan

address: Via Amedeo, 42

department: Department of Diagnostic Innovation

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: Elig30-3-3

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed using HTSeq-count.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts for each Sample

extract_protocol:
RNA was extracted from untreated HepG2 cells and from HepG2 cells treated with Eliglustat (20 or 30 µM) for 72 h using the Maxwell® RSC RNA FFPE Kit (Cat. No. AS1440, Promega Corporation, Madison, WI, USA) on a semi-automated Maxwell® RSC instrument (Promega). RNA concentration was measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was assessed using the Agilent 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus Kit (Illumina, San Diego, CA, USA; Cat. No. 20040525), according to the manufacturer's instructions. Briefly, libraries were generated from 100 ng of total RNA. Ribosomal RNA (rRNA) was first depleted, and the remaining RNA was reverse-transcribed into cDNA. Adapter ligation and PCR amplification were subsequently performed to generate sequencing-ready libraries. Library concentrations were measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and library quality was assessed using the Agilent 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA). All libraries were purified, pooled, and diluted to a final concentration of 0.5 nM. Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) using a NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles) to generate paired-end 2 × 75 bp reads.

value: Eliglustat 30µM


title: cCeO_bRG2_ATAC-seq

description:
Library name: 110599
GEO_chimp_ATAC_counts.tsv.gz
cCeO_bRG_consensusPeak.narrowPeak.gz


title: DD1071


title: M5

description:
Library name: M5
DAP-seq


title: cCeO_aRG2_ATAC-seq

description:
Library name: 110598
GEO_chimp_ATAC_counts.tsv.gz
cCeO_aRG_consensusPeak.narrowPeak.gz


title: M4

description:
Library name: M4
DAP-seq


title: DD1069


title: HepG2, Eliglustat30, rep2

description: Library name: Elig30-3-2


title: cCeO_N1_ATAC-seq

description:
Library name: 107337
GEO_chimp_ATAC_counts.tsv.gz
cCeO_N_consensusPeak.narrowPeak.gz


title: HepG2, Eliglustat30, rep1

description: Library name: Elig30-3-1


title: M3

description:
Library name: M3
DAP-seq


title: DD1055


title: cCeO_bIP1_ATAC-seq

description:
Library name: 107336
GEO_chimp_ATAC_counts.tsv.gz
cCeO_bIP_consensusPeak.narrowPeak.gz


title: HepG2, Eliglustat20, rep3

description: Library name: Elig20-3-3

value: Eliglustat 20µM


title: DD1054


title: cCeO_bRG1_ATAC-seq

description:
Library name: 107335
GEO_chimp_ATAC_counts.tsv.gz
cCeO_bRG_consensusPeak.narrowPeak.gz

value: cerebral organoid


title: M2

description:
Library name: M2
DAP-seq


title: M18

description:
Library name: M18
DAP-seq


title: DD0728


title: HepG2, Eliglustat20, rep2

description: Library name: Elig20-3-2


title: HepG2, Eliglustat20, rep1

description: Library name: Elig20-3-1


title: M17

description:
Library name: M17
DAP-seq


title: HepG2, control, rep3

description: Library name: CONTROL-3-3

value: control


title: M16

description:
Library name: M16
DAP-seq


title: DD_LG811


title: ALT479

value: Well-differentiated

value: extremity


title: A549 cells treated with 20 mM lactic acid for 24 h, biological replicate 2

city: chendu

first: lilan

last: he

address: yulin

institute: Sichuan University

description:
Library name: A549_LAC_2
Lactic-acid-treated biological replicate 2; 150-bp paired-end sequencing; matrix column: LAC-2 in All_gene_counts.txt and All_gene_fpkm.txt

data_processing:
Raw reads were filtered using in-house Perl scripts to remove adapter-containing reads, poly-N reads, and low-quality reads. Q20, Q30, and GC content were calculated.
Clean paired-end reads were aligned to the Homo sapiens reference genome Homo_sapiens.GRCh38_release95.genome.fa using HISAT2.
StringTie was used to assemble mapped reads and quantify gene and transcript expression as FPKM values.
Gene-level read counts were used for differential expression analysis between the lactic-acid and PBS-control groups with DESeq2. Genes with fold change ≥ 2 and FDR < 0.01 were considered differentially expressed.
Assembly: GRCh38, Ensembl Homo sapiens reference genome release 95
Supplementary files format and content: All_gene_counts.txt is a tab-delimited plain-text file containing gene-level raw read counts for NS-1, NS-2, NS-3, LAC-1, LAC-2, and LAC-3, together with gene identifiers.
Supplementary files format and content: All_gene_fpkm.txt is a tab-delimited plain-text file containing gene-level FPKM values for NS-1, NS-2, NS-3, LAC-1, LAC-2, and LAC-3, together with gene identifiers.

growth_protocol: A549 cells were maintained under standard cell-culture conditions prior to treatment.

extract_protocol:
Total RNA was extracted from A549 cells using TRIzol reagent according to the manufacturer's instructions. RNA samples were submitted to a commercial sequencing service for quality assessment, library preparation, and sequencing.
Poly(A)+ mRNA was enriched using oligo(dT)-coupled magnetic beads. Sequencing libraries were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, catalog no. 13533ES96) according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq X Plus platform to generate 150-bp paired-end reads (PE150).

treatment_protocol: A549 cells were treated with 20 mM lactic acid added directly to the culture medium for 24 h. Control cells received an equal volume of PBS for 24 h.

value: 20 mM lactic acid was added directly to the culture medium for 24 h


title: M15

description:
Library name: M15
DAP-seq

value: Klebsiella pneumoniae


title: RNASeq_144 06_60_T_d23

city: Cambridge

first: Richard

middle: Lee

last: Gieseck III

address: 1 Portland St.

institute: Pfizer, Inc.

description:
Library name: 06_60_T_d23
study day=23; RIN=6.2; tumor_volume_mm3=320.90744; sample_status=RNAlater

data_processing:
STAR Alignment v020201
bcl2fastq2 v2.20
RSEM v1.3.0
TPM and normalization using Data4Cure Biomedical Intelligence Cloud
Assembly: mm10
Supplementary files format and content: Tab-delimited matrix of log2(TPM) values by gene (HGNC filtered).

source_name: Tumor

growth_protocol: CT26 tumor-bearing BALB/c mouse study; tissue harvested at study day 16 or 23.

extract_protocol:
Total RNA extracted from collected tissues (spleen, tumor, TDLN) using study SOP.
Paired-end stranded mRNA-seq library prep with polyA enrichment.

treatment_protocol: Treatments include Isotype, PD1, CYTO, PD1/CYTO, TS/CYTO, and TS/PD1/CYTO per study design.

value: Tumor

value: BALB/c


title: A549 cells treated with 20 mM lactic acid for 24 h, biological replicate 1

description:
Library name: A549_LAC_1
Lactic-acid-treated biological replicate 1; 150-bp paired-end sequencing; matrix column: LAC-1 in All_gene_counts.txt and All_gene_fpkm.txt


title: RNASeq_144 06_60_TDLN_d23

description:
Library name: 06_60_TDLN_d23
study day=23; RIN=6.8; tumor_volume_mm3=320.90744; sample_status=RNAlater

source_name: Tumor draining lymph node

value: Tumor draining lymph node


title: Homo sapiens,NC_IP RNA

city: Nanjing

first: Tingting

last: Xu

address: Guangzhou Road 303

institute: The first affiliated hospital of Nanjing Medical University

description: Library name: NC_1_IP

data_processing:
Raw paired-end sequencing reads were processed using fastp (version 0.19.4; https://github.com/OpenGene/fastp) to obtain high-quality clean reads. Reads containing adapter sequences, poly(A) or poly(G) sequences, or more than 5% undetermined nucleotides (N) were removed. Reads in which more than 20% of bases had a Phred quality score of ≤20 were also discarded.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes integrated analysis results of MeRIP-seq and RNA-seq data comparing the metll16 Overexpression (OE) group versus the Negative Control (NC).
Library strategy: MeRIP-Seq

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. The quantity and purity of RNA from each sample were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).
Ribosomal RNA (rRNA) was depleted from total RNA using the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, CA, USA). The resulting rRNA-depleted RNA was fragmented at 86°C for 7 min using the NEBNext Magnesium RNA Fragmentation Module (NEB, cat. E6150S, USA). The fragmented RNA was subjected to m6A immunoprecipitation using an m6A-specific antibody (Synaptic Systems, cat. 202003, Germany) coupled to Dynabeads with the Dynabeads Antibody Coupling Kit (Thermo Fisher Scientific, CA, USA). Immunoprecipitation was performed in IP buffer containing 50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630. The immunoprecipitated RNA and corresponding input RNA were reverse-transcribed into cDNA using SuperScript II Reverse Transcriptase (Invitrogen, cat. 1896649, USA). Second-strand cDNA synthesis was performed using E. coli DNA Polymerase I (NEB, cat. M0209, USA), RNase H (NEB, cat. M0297, USA), and dUTP Solution (Thermo Fisher Scientific, cat. R0133, USA). Following end repair and A-tailing, dual-index adapters were ligated, and fragments were size-selected and purified using AMPure XP beads. The dUTP-containing second strand was digested using heat-labile UDG (NEB, cat. M0280, USA). The adapter-ligated products were amplified by PCR under the following conditions: initial denaturation at 95°C for 3 min; 8 cycles of 98°C for 15 s, 60°C for 15 s, and 72°C for 30 s; followed by a final extension at 72°C for 5 min. Libraries with an approximate fragment size of 300 ± 50 bp were sequenced on an Illumina NovaSeq 6000 platform (LC-Bio Technology Co., Ltd., Hangzhou, China) using 150-bp paired-end sequencing.

value: epithelial cell

value: transfected with empty control plasmid


title: M13

description:
Library name: M13
DAP-seq

value: strain

value: genotype

value: WT

value: ChIP antibody


title: RNASeq_144 06_60_S_d23

description:
Library name: 06_60_S_d23
study day=23; RIN=9.0; tumor_volume_mm3=320.90744; sample_status=RNAlater

source_name: Spleen

value: Spleen


title: Homo sapiens,NC_input RNA

description: Library name: NC_1_input


title: RNASeq_144 06_59_T_d23

description:
Library name: 06_59_T_d23
study day=23; RIN=5.6; tumor_volume_mm3=2198.2675; sample_status=RNAlater


title: A549 cells treated with PBS for 24 h, control biological replicate 2

description:
Library name: A549_NS_2
Control biological replicate 2; 150-bp paired-end sequencing; matrix column: WT-2 in All_gene_counts.txt and All_gene_fpkm.txt

value: An equal volume of PBS was added to the culture medium for 24 h


title: A549 cells treated with PBS for 24 h, control biological replicate 1

description:
Library name: A549_NS_1
Control biological replicate 1; 150-bp paired-end sequencing; matrix column: WT-1 in All_gene_counts.txt and All_gene_fpkm.txt


title: Homo sapiens,metll16 OE_IP RNA

description: Library name: OE_1_IP


title: RNASeq_144 06_59_TDLN_d23

description:
Library name: 06_59_TDLN_d23
study day=23; RIN=4.5; tumor_volume_mm3=2198.2675; sample_status=RNAlater


title: FRPBiopsy_13_Female_MASLD

city: Edinburgh

first: Eleni

last: Papachristoforou

address: Edinburgh BioQuarter 4-5 Little France Drive

department: Institute for Regeneration and Repair

institute: University of Edinburgh

description:
Library name: FRPBiopsy_13
10X Genomics scRNAseq FLEX

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs was performed using 'cellranger multi' (Cell Ranger 7.0.0), and a csv specifying the probe barcode. Genome build: Human GRCh38-2020-A
Conversion of per-sample BAM files from CellRanger to per-sample fastq files using  'cellranger bamtofastq' Cell Ranger 7.0.0
Assembly: Human GRCh38-2020-A
Supplementary files format and content: mtx: count matrix in sparse matrix format (CellRanger output)
Supplementary files format and content: barcodes.tsv: barcode ids per sample (CellRanger output)
Supplementary files format and content: genes.tsv: gene ids per sample (CellRanger output)

source_name: Liver

extract_protocol:
Liver needle biopsies were taken from patients and immediately snap-frozen. Samples were fixed and cells isolated using the ChromiumTM Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics, 1000414) according to the 10X Genomics demonstrated protocol (document number CG000553).
scRNA-seq and library preparation was performed using ChromiumTM Next GEM Single Cell Fixed RNA Hybridization & Library Kit (10X Genomics, PN-1000415), ChromiumTM Single Cell Fixed RNA Human Transcriptome Probe Kit and Chromium Next GEM Chip Q Kit (10X Genomics, PN-2000518) on the ChromiumTM X Single Cell Platform (10X Genomics), according to manufacturer’s protocol.

value: Liver

tag: Sex

value: Female

tag: disease state

value: MASLD

tag: probe barcode


title: RNASeq_144 06_59_S_d23

description:
Library name: 06_59_S_d23
study day=23; RIN=8.8; tumor_volume_mm3=2198.2675; sample_status=RNAlater


title: Homo sapiens,metll16 OE_input RNA

description: Library name: OE_1_input


title: Mir-31 knockout human iPS cell-derived cardiomyocytes 2

city: Indianapolis

first: Lei

last: Yang

state: IN

address: 1044 W Walnut Street

institute: Indiana University School of Medicine

description: Library name: 4_31KO-CM_S40

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE 31 genes using featureCounts (from subread v2.0.1).
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.38.4).
Assembly: hg38
Supplementary files format and content: raw counts, text file

source_name: Cardiomyocytes

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were cultured on Matrigel (BD Biosciences)-coated plates in mTesR1 medium.

extract_protocol:
Total RNAs were extracted by using the RNeasy Kit (Qiagen, USA), followed with QC by using an Agilent Bioanalyzer 2100.
One hundred nanograms of total RNAs were used for cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors and amplification, by following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352-v4.17 (Roche Corporate). Each resulting indexed library was quantified and its quality was accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity.

treatment_protocol: For cardiomyocyte differentiation, the monolayer differentiationmethod was used based on a published protocol (Lian et al., 2013). After 14 days of differentiation, DMEM medium (no glucose) with 4 mM lactate (Sigma, #CAT-L1750-10G) was used to enrich cardiomyocytes according to the published protocol (Tohyamaet al., 2013).

value: Cardiomyocytes

value: miR-31 KO iPS cells

value: miR-31 KO


title: L9

description:
Library name: L9
DAP-seq

value: Klebsiella pneumoniae


title: RNASeq_144 06_58_TDLN_d23

description:
Library name: 06_58_TDLN_d23
study day=23; RIN=7.2; tumor_volume_mm3=175.139604; sample_status=RNAlater

value: BALB/c


title: FRPBiopsy_11_Male_MASLD

description:
Library name: FRPBiopsy_11
10X Genomics scRNAseq FLEX

value: Male


title: Mir-31 knockout human iPS cell-derived cardiomyocytes 1

description: Library name: 3_31KO-CM_S37


title: L8

description:
Library name: L8
DAP-seq


title: RNASeq_144 06_58_S_d23

description:
Library name: 06_58_S_d23
study day=23; RIN=7.6; tumor_volume_mm3=175.139604; sample_status=RNAlater


title: Control normal human iPS cell-derived cardiomyocytes 2

description: Library name: 2_WT-CM_S39

value: human iPS cells


title: RNASeq_144 06_52_T_d23

description:
Library name: 06_52_T_d23
study day=23; RIN=6.3; tumor_volume_mm3=180.801848; sample_status=Fresh-frozen

value: Tumor


title: L7

description:
Library name: L7
DAP-seq

value: strain


title: FRPBiopsy_10_Female_MASLD

description:
Library name: FRPBiopsy_10
10X Genomics scRNAseq FLEX


title: FRPBiopsy_09_Male_MASLD

description:
Library name: FRPBiopsy_09
10X Genomics scRNAseq FLEX


title: Control normal human iPS cell-derived cardiomyocytes 1

description: Library name: 1_WT-CM_S36


title: L6

description:
Library name: L6
DAP-seq

value: genotype


title: RNASeq_144 06_36_TDLN_d16

description:
Library name: 06_36_TDLN_d16
study day=16; RIN=7.8; tumor_volume_mm3=292.396716; sample_status=RNAlater

value: Tumor draining lymph node


title: RNASeq_144 06_35_TDLN_d16

description:
Library name: 06_35_TDLN_d16
study day=16; RIN=7.9; tumor_volume_mm3=183.438936; sample_status=RNAlater


title: L5

description:
Library name: L5
DAP-seq

value: WT

value: ChIP antibody


title: MAC-PD patient peripheral blood, biological replicate 5

city: Shanghai

first: Guoling

address: No. 507 Zhengmin Road

department: Department of Tuberculosis

institute: Shanghai Pulmonary Hospital

description:
Library name: MAC5
Bulk RNA-seq of peripheral blood from MAC subject

data_processing:
Raw sequencing reads were quality-controlled, adapters were trimmed, and clean reads were aligned to the human reference genome (GRCh38). Gene-level read counts were quantified.
Assembly: GRCh38 (Homo sapiens)
Supplementary files format and content: GSE_bulk_RNAseq_gene_counts_matrix.txt.gz: tab-delimited text file containing a gene-level raw read count matrix; rows are genes (Ensembl gene IDs), columns are samples. DGE_DGE-MAB_vs_HC.txt.gz, DGE_DGE-MAC_vs_HC.txt.gz and DGE_DGE-MA_vs_HC.txt.gz: tab-delimited text files of differential gene expression results (Gene_ID, Symbol, log2FoldChange, Pvalue, FDR) for each comparison.

source_name: peripheral blood

extract_protocol:
Total RNA was isolated from peripheral blood using the RNAmini kit (Qiagen, Germany). RNA quality was assessed by gel electrophoresis and Qubit fluorometry (Thermo, Waltham, MA, USA).
Strand-specific libraries were constructed with the Stranded mRNA-seq (NR602) kit (Vazyme, Nanjing, China) and sequenced on an Illumina NovaSeq 6000 in 150 bp paired-end mode to generate raw reads.

value: peripheral blood

value: MAC-PD patient


title: FRPBiopsy_07_Female_MASLD

description:
Library name: FRPBiopsy_07
10X Genomics scRNAseq FLEX

value: Liver

value: Female


title: MAC-PD patient peripheral blood, biological replicate 4

description:
Library name: MAC4
Bulk RNA-seq of peripheral blood from MAC subject


title: L4

description:
Library name: L4
DAP-seq


title: RNASeq_144 06_34_TDLN_d16

description:
Library name: 06_34_TDLN_d16
study day=16; tumor_volume_mm3=253.110096; sample_status=RNAlater


title: FRPBiopsy_06_Male_Healthy

description:
Library name: FRPBiopsy_06
10X Genomics scRNAseq FLEX

value: Healthy


title: MAC-PD patient peripheral blood, biological replicate 3

description:
Library name: MAC3
Bulk RNA-seq of peripheral blood from MAC subject


title: L3

description:
Library name: L3
DAP-seq


title: RNASeq_144 05_50_T_d23

description:
Library name: 05_50_T_d23
study day=23; RIN=5.7; tumor_volume_mm3=1170.59334; sample_status=RNAlater

value: TS/CYTO


title: MAC-PD patient peripheral blood, biological replicate 2

description:
Library name: MAC2
Bulk RNA-seq of peripheral blood from MAC subject


title: FRPBiopsy_05_Female_Healthy

description:
Library name: FRPBiopsy_05
10X Genomics scRNAseq FLEX


title: L20

description:
Library name: L20
DAP-seq


title: RNASeq_144 05_50_TDLN_d23

description:
Library name: 05_50_TDLN_d23
study day=23; RIN=6.2; tumor_volume_mm3=1170.59334; sample_status=RNAlater


title: FRPBiopsy_04_Male_Healthy

description:
Library name: FRPBiopsy_04
10X Genomics scRNAseq FLEX


title: MAC-PD patient peripheral blood, biological replicate 1

description:
Library name: MAC1
Bulk RNA-seq of peripheral blood from MAC subject


title: FRPBiopsy_03_Female_Healthy

description:
Library name: FRPBiopsy_03
10X Genomics scRNAseq FLEX


title: L19

description:
Library name: L19
DAP-seq


title: RNASeq_144 05_49_T_d23

description:
Library name: 05_49_T_d23
study day=23; RIN=4.5; tumor_volume_mm3=1097.391456; sample_status=RNAlater


title: FRPBiopsy_02_Male_Healthy

description:
Library name: FRPBiopsy_02
10X Genomics scRNAseq FLEX


title: MAB-PD patient peripheral blood, biological replicate 4

description:
Library name: MAB4
Bulk RNA-seq of peripheral blood from MAB subject

value: MAB-PD patient


title: L18

description:
Library name: L18
DAP-seq

value: Klebsiella pneumoniae


title: RNASeq_144 05_49_TDLN_d23

description:
Library name: 05_49_TDLN_d23
study day=23; RIN=6.5; tumor_volume_mm3=1097.391456; sample_status=RNAlater

value: BALB/c


title: FRPBiopsy_01_Male_Healthy

description:
Library name: FRPBiopsy_01
10X Genomics scRNAseq FLEX

value: Male