title: SKCO1 cells, Pan-KRAS siRNA, 24 hrs, Biol Rep 3

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq quantification with STAR/Salmon workflow.
Reads were mapped to GRCh38 using STAR 2.7.6a (parameters: --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM).
Quantification of transcripts (gene-level) was performed using Salmon 1.4.0, based on the human transcriptome defined by GENCODE, Release 22.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes Salmon-quantification of transcripts (gene-level) for each sample.

growth_protocol: SKCO1 cells were maintained in DMEM supplemented with 10% FBS in humidified atmosphere with 5% CO2 and 37C.

extract_protocol:
RNA was extracted using the Quick RNA Mini Prep kit (Zymo Research).
mRNAseq libraries were created from up to 1000 ng of total RNA using a TruSeq Stranded mRNA Library Prep Kit (Illumina 20020595) following the manufacturer’s protocol (Illumina 1000000040498). Libraries were created using a Hamilton NGS STAR automated liquid handler.

treatment_protocol: SKCO1 cells were transfected siRNAs at 20 nM with Lipofectamine RNAiMAX following manufacturer's protocol and RNA was collected after 24 hours.

value: colorectal adenocarcinoma

value: KRAS knockdown

value: transfection, Pan-KRAS siRNA

tag: time

value: 24 hrs


title: hep-D biol rep 1

status: Public on Jul 16 2025

type: SRA

city: Guangzhou

first: Wu

last: Haibin

address: Waihuan east road

country: China

institute: South china university of technology

library_source: transcriptomic

data_processing:
Sequencing was performed by Novogene (China) on an Illumina HiSeq X-Tensequencer with 150 bp paired- end sequencing reaction.
The reads were mapped to the human reference genome using HISAT2.
Reads Counts for each gene in each sample were counted by featureCounts, and FPKM (Fragments Per Kilobase Millon Mapped Reads) and then were calculated to estimate the expression level of genes in each sample.
Assembly: GRCh38
Supplementary files format and content: raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: P-heporgs

extract_protocol:
Total RNA of  HB-orgs and P-hep-orgs  were extracted using RNAiso Plus kit according to the manufacturer’s instructions.
The cDNA libraries for RNA sequencing were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB).

tag: cell type

value: H9 differentiated cells

value: P-heporgs

tag: treatment

value: dynamic condition


title: HB-S biol rep 3

source_name: HB-orgs

value: HB-orgs

value: static condition


title: 10, skin, allergic contact dermatitis, methylisothiazolinone

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Library name: 10

data_processing:
Reads were mapped with STAR software (v.2.7.8a) against the human reference genome GRCh38 using the GRCh38.p13 Ensembl annotation.
The table of counts was obtained with featureCounts function in the package subread (v.2.0.3).
Counts were normalized with log2 counts per million (CPM) with the edgeR package (v.3.40.2) with a prior.count=3. Genes with more than 10 counts in at least 9 samples were kept.
Assembly: GRCh38
Supplementary files format and content: counts

source_name: skin

growth_protocol: Skin biopsies were incubated with RNAlater during maximum 1 week

extract_protocol:
Total RNA was extracted from  skin biopsies with Genelute mammalian total RNA kit from Sigma- Aldrich (cat. No. RTN350). Tissue was disrupted and digested in the Lysis buffer with proteinase K (P4850, Sigma-Aldrich) and 2-mercaptoethanol (M3148, Sigma-Aldrich) incubating it for 10 minutes at 55ºC.  After washing and centrifugation several times to remove contaminants, RNA was eluted with 50 μl of Elution buffer. Two commercial kits were tested. This kit obtained the best performance in total RNA recovered and integrity of the sample. The samples were used immediately or stored at -80ºC for future use.
Samples were processed according to Truseq RNA Exome protocol from Illumina (Document #10000000039582 v01 March 2018) following steps from 1 to 6_Enrich DNA Fragments page 18. Afterwards, samples were processed using Illumina RNA preparation with enrichment Tagmentation protocol (Document #1000000124435 v03 April 2021) following steps from 6_Normalize Library page 15 to the end of the protocol. Samples were enriched with Illumina Exome Panel and Unique Dual Index from NEBNext were used. The initial total RNA input for every sample was 100 nanograms measured with Qubit 4.0. 200 nanograms of each amplified sample was enriched in pools up to 3 samples, libraries profiles were checked by 2100 Bioanalyzer. All samples amplified enough to continue with the process. Final enriched libraries were quantified by 2100 Bioanalyzer (DNA 1000 kit). Samples were sequenced in a NextSeq2000 from Illumina with an estimated output of 25 million reads/sample and a read length of 2x50bp.
Exome RNA capture

treatment_protocol: No other treatments other than keeping in RNAlater

tag: tissue

value: skin

tag: condition

value: allergic contact dermatitis

tag: allergen

value: methylisothiazolinone

tag: age

tag: batch

tag: technician

value: C

tag: Sex

value: female


title: LTbRAb_6

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

country: USA

institute: Johns Hopkins All Children's Hispital

description:
ST#23 C anti-LTbR Ab-6
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as follows:
1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases.
After the removal of the reads that contained adaptor contamination, low quality bases, and undetermined bases by Cutadapt, sequence quality was verified using FastQC. HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/, StringTie was used for assembled. To estimate the expression levels of all transcripts, StringTie and ballgrwn were used. The mRNA differential expression analysis was performed by R package DESeq2 between two different groups (and by R package edgeR between two samples). The mRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed mRNAs. The heatmap was generated with the top 100 genes exhibiting the most significant FDR in DESeq2 analysis. Z scores of the normalized value were applied to pheatmap package (version=1.0.12).
Partek Flow software was used for following data processing and analysis. Raw data was trimmed,  alignment by STAR with mm39 - Ensembl Transcripts release 108 , Gene count was further normalized by DEseq2.
Assembly: mm39 - Ensembl Transcripts release 108
Supplementary files format and content: "Partek_ST_23Normalized_counts.csv" : normalized count of DEseq2 was caliculated and shown in the file  "Partek_ST_23Normalized_counts.csv"
Supplementary files format and content: "counts.txt" : Experiment #ST#15 and #ST#23 has been processed for batch collection by General linear model Batch effect adjustment on PartekFlow software. Normalized count of DEseq2 was caliculated. Data is shown in  "counts.txt".
Supplementary files format and content: " gene_list.txt": GSEA from combined data of ST#15 amd ST#23 has been caliculated on Partek Flow software as B ADU-S100 vs A control, C anti-LTbRAb vs A control, D combination vs A control. Gene list and GSEA data is shown as " gene_list.txt"

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Mouse tumors from KxPxCx injection

value: anti-LTbRAb


title: SKCO1 cells, Pan-KRAS siRNA, 24 hrs, Biol Rep 2

tag: cell line

tag: genotype


title: LTbRAb_5

description:
ST#23 C anti-LTbR Ab-5
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: HB-S biol rep 1


title: HB-S biol rep 2


title: 14, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 14


title: LTbRAb_4

description:
ST#23 C anti-LTbR Ab-4
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: HB-D biol rep 3


title: SKCO1 cells, EFTX-G12V siRNA, 24 hrs, Biol Rep 3

value: KRAS-G12V knockdown

value: transfection, EFTX-G12V siRNA


title: C_V3

city: Jinan

first: wenqiao

last: jia

state: Shandong

address: 107 Wenhua Xilu

department: Department of Health Management Center

institute: Qilu Hospital of Shandong University

description: Library name: C_V3

data_processing:
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
After obtaining clean reads, we use HISAT2 to align clean reads to the reference genome sequence. Bowtie2 is used to align clean reads to the reference gene sequence to obtain alignment results.
Assembly: hg38
Supplementary files format and content: csv files include reads count for each sample

extract_protocol:
The total RNA was extracted from the cultured cells by the TRIzol regents (Invitrogen, Carlsba d, CA, USA) to break open the cells and release the RNA.
We performed RNA-seq analyses (ShenZhen BGI Genomics Co., Ltd. China) to compared the mRNA expression profiles between control (Vector) and PCP4 overexpression (PCP4) C4-2B cells.

treatment_protocol: Lentiviral vectors encoding PCP4 and the empty vector control were procured from (Genechem, China) and the infection procedure was carried out in strict accordance with the manufacturer’s instruction.

value: Human prostate cancer cell

value: Transfected with negative control vector


title: C_V2

description: Library name: C_V2


title: LTbRAb_3

description:
ST#23 C anti-LTbR Ab-3
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: SKCO1 cells, EFTX-G12V siRNA, 24 hrs, Biol Rep 2

value: colorectal adenocarcinoma

value: 24 hrs


title: LTbRAb_1

description:
ST#23 C anti-LTbR Ab-1
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LpaLO_3_LPS

city: Ann Arbor

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

institute: University of Michigan

description: Single RNA

data_processing:
RNA was sequenced using Illumina NextSeq (HO) 150 cycle Sequencing.
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Reference and Annotation: GRCh38 from ENSEMBL
Assembly: GRCh38 from ENSEMBL
Supplementary files format and content: tab delimited text file of Raw counts of each smples  Generated using Bioconductor R package Rsubread and featureCounts function
Supplementary files format and content: tab delimited text file of counts per million of each smples

source_name: Blood

extract_protocol:
Cells were lysed with RLT Plus Buffer (QIAGEN, Cat. No. 1053393)followed by RNA purifcationusing RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to manufacturer’s protocol.
RNA-seq libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen; Cat. No. 015) with the UMI add-on kit.

treatment_protocol: PBMC from both highsubjects (n = 6) and low Lp(a)subjects (n = 3) were stimulated  with the TLR4 ligand LPS (1 ug /ml for 2 hours).TLR ligand (LPS) were obtained from InvivoGen

value: Blood

value: peripheral blood mononuclear cells

tag: disease state

value: Lp(a) control/Lp(a) low

value: TLR4 ligand LPS (1 mg /ml for 2 hours)


title: 23DMSO24

type: RNA

description: Gene expression data from RH4 cell line treate with vehicle

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Human array using an Affymetrix GeneChip Hybridization Oven 645.

scan_protocol: GeneChip WT  PLUS Reagent kit (P/N 703174 2017) and Expression Wash, Stain and Scan User Manual (P/N  702731 2017) (Affymetrix Inc., Santa Clara, CA, USA).

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples.

label: Biotin

source_name: RH4 cell line_Control

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Cell were cultured in RPMI 1640 medium supplemented with 10% of fetal bovine serum (FBS), with of L-glutamine and penicilin-streptomycin following standard protocol. Cells grew in monolayer conditions. Cell Culures were anteindes at 37ºC in humdified atmosphere.

extract_protocol: RNA was isolated and purified with the RNeasy Mini Kit (Qiagen)

treatment_protocol: Vehicle (DMSO) or Ipatasertib (1µM) or Miransertib (1µM).

tag: agent

value: DMSO


title: 23IPA24

description: Gene expression data from RH4 cell line treate with Ipatasertib_24h

source_name: RH4 cell line_Ipa_24h

value: IPA


title: 17DMSO24


title: SKCO1 cells, EFTX-G12V siRNA, 24 hrs, Biol Rep 1


title: 23MIR24

description: Gene expression data from RH4 cell line treate with Miransertib_24h

source_name: RH4 cell line_Mir_24h

value: MIRA


title: C_V1

description: Library name: C_V1


title: 17IPA24


title: C_P2

description: Library name: C_P2

value: Transfected with expression vector containing PCP4


title: LTbRAb_2

description:
ST#23 C anti-LTbR Ab-2
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: SKCO1 cells, Pan-KRAS siRNA, 24 hrs, Biol Rep 1

value: KRAS knockdown

value: transfection, Pan-KRAS siRNA


title: C_P3

description: Library name: C_P3


title: HB-D biol rep 2

value: H9 differentiated cells

value: HB-orgs

value: dynamic condition


title: SKCO1 cells, Neg Ctrl siRNA, 24 hrs, Biol Rep 2

value: WT

value: transfection, negative control siRNA


title: 17MIR24


title: S100_6

description:
ST#23 B ADU-S100-6
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt

value: Mouse tumors from KxPxCx injection


title: LpaLO_3_NT

description: Single RNA

value: No treatment


title: Monocrotaline-Exercised replicate 6

city: College Station

first: Mariana

middle: Janini

last: Gomes

state: TX

address: 2929 Research Pkwy

department: Health and Kinesiology

institute: Texas A&M University

description: Library name: 14_4596_42B_S14

data_processing:
Reads were trimmed of low-quality (Phred <20), adapter, and barcode sequences using Trim-Galore
Sequences were aligned to the Rattus norvegicus transcriptome (En-sembl mRatBN7.2.112) and quantified at the transcript level using Salmon
transcript-level abundances generated by Salmon were collapsed down to the gene level using the “tximport” package from BioconductoR, by a transcript-to-gene mapping built using the R. norvegicus (Ensembl mRatBN7.2.112) GFF3 annotation file with the “txdbmaker” BioconductoR package.
Statistical testing was conducted with DESeq2 (v1.44.0). Significant genes were defined as those with an adjusted p-value < 0.05 (BH corrected, Wilcoxon p-test) and a log2 fold-change magnitude of 1 or greater. Pathway enrichment was carried out using clusterProfiler (v4.12.6) with both Kyoto Encyclopedia of Gene and Genomes (KEGG) [17, 18] and Gene Ontology (GO) [16] en-richment analysis for R. norvegicus pathway databases with a p-adjusted value <0.05 (BH corrected).
Assembly: mRatBN7.2
Supplementary files format and content: Raw counts of Salmon mapped reads for all samples in a single csv file

organism: Rattus norvegicus

source_name: Rat gastrocnemius muscle

extract_protocol:
Total RNA was extracted from 30mg of frozen medial gastrocnemius (left leg) of six samples per group using the RNeasy® Plus Universal mini kit (QIAGEN) following the manufacturer’s instruction. Total RNA quality was assessed using the Agilent TapeStation, and all samples had RNA integrity numbers (RIN) greater than 8. RNA quantification was performed with the Qubit RNA BR Assay Kit
Poly-A-based RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep Kit with 650ng of RNA input per sample, following the manufacture’s protocol. Library quality and size distribution (average size: 340-360bp) were confirmed using the Agilent TapeStation.

value: Rat gastrocnemius muscle


title: SKCO1 cells, Neg Ctrl siRNA, 24 hrs, Biol Rep 3

value: colorectal adenocarcinoma

value: 24 hrs


title: S100_8

description:
ST#23 B ADU-S100-8
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: S100_7

description:
ST#23 B ADU-S100-7
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: C_P1

description: Library name: C_P1

value: Human prostate cancer cell


title: LpaLO_2_LPS

description: Single RNA

value: Blood

value: peripheral blood mononuclear cells

value: Lp(a) control/Lp(a) low

value: TLR4 ligand LPS (1 mg /ml for 2 hours)


title: Monocrotaline-Exercised replicate 5

description: Library name: 10_4596_34B_S10


title: LpaLO_2_NT

description: Single RNA


title: S100_4

description:
ST#23 B ADU-S100-4
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: Monocrotaline-Exercised replicate 4

description: Library name: 5_4596_28B_S5


title: LpaLO_1_LPS

description: Single RNA


title: S100_3

description:
ST#23 B ADU-S100-3
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LpaLO_1_NT

description: Single RNA


title: LpaHI_6_LPS

description: Single RNA

value: Lp(a) high


title: S100_2

description:
ST#23 B ADU-S100-2
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: HB-D biol rep 1


title: LCC9_4_OHT_3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Sequencing was performed on the Illumina NextSeq 2000 platform using a P3 100 cycle reagent kit with a P3 flow cell
Libraries were sequenced with a single 101 cycle read length with 2 index reads of 10bp each.  FASTQ files were generated utilizing BaseSpace illumina-inc. basespace-dragen-analysis.1.3.0.
FASTQ files were generated utilizing BaseSpace illumina-inc. basespace-dragen-analysis.1.3.0
Quality control (QC) of the raw sequence data was performed using FastQC
The sequencefiles were directly aligned to the Human reference genome assembly (hg38.p12) using STAR (version 2.6), generating alignment files in bam format
Raw gene counts were determined using HTSeq v0.10.0 with the Ensembl v93 hg38 annotations
Assembly: hg38.p12
Supplementary files format and content: tab-delimited text file of HTSeq generated raw counts

growth_protocol: MCF-7 and LCC9 BC cells were maintained in IMEM and supplemented with 10% FBS (MCF-7) or 5% FBS (LCC9) and 1% Pen/Strep with 5%CO2 ar 37C

extract_protocol:
PolyA+ mRNA was isolated according to manufacturer’s instructions using the Dynabeads mRNA Direct Purification Kit
Libraries were prepped using 50 ng total RNA per sample with Illumina Stranded mRNA Library Prep

treatment_protocol: All BC cells were serum starved in IMEM -Phenol Red-free medium, supplemented with 5% DCC-FBS and 1% PS for 72 h prior to treatment. Following 72 h incubation in SS media, the cells were treated with vehicle control (DMSO), or 100 nM 4-OHT for 24 h in SS media

value: TAM-resistant MCF-7 derivitive


title: SKCO1 cells, Neg Ctrl siRNA, 24 hrs, Biol Rep 1


title: LCC9_4_OHT_5


title: S100_5

description:
ST#23 B ADU-S100-5
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LCC9_4_OHT_4


title: LCC9_4_OHT_2


title: Monocrotaline-Exercised replicate 3

description: Library name: 3_4596_23B_S3


title: Monocrotaline-Exercised replicate 2

description: Library name: 2_4596_22B_S2


title: LCC9_DMSO_5

value: DMSO (Control)


title: LpaHI_6_NT

description: Single RNA


title: Cont_8

description:
ST#23 A control-8
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt

value: Control


title: LpaHI_5_NT

description: Single RNA


title: LCC9_DMSO_4


title: Cont_7

description:
ST#23 A control-7
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LCC9_4_OHT_1


title: S100_1

description:
ST#23 B ADU-S100-1
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: Monocrotaline-Exercised replicate 1

description: Library name: 1_4596_21B_S1


title: Monocrotaline-Sedentary replicate 5

description: Library name: 18_4596_50B_S18


title: LCC9_DMSO_3


title: LpaHI_4_LPS

description: Single RNA


title: Cont_6

description:
ST#23 A control-6
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LpaHI_4_NT

description: Single RNA


title: Monocrotaline-Sedentary replicate 3

description: Library name: 8_4596_32B_S8


title: LCC9_DMSO_2


title: Monocrotaline-Sedentary replicate 4

description: Library name: 12_4596_38B_S12


title: Cont_5

description:
ST#23 A control-5
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LCC9_DMSO_1


title: Cont_4

description:
ST#23 A control-4
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: LpaHI_3_LPS

description: Single RNA


title: MCF_7_4_OHT_5

value: Breast Cancer Luminal A subtype


title: LpaHI_3_NT

description: Single RNA


title: LpaHI_2_LPS

description: Single RNA


title: Cont_2

description:
ST#23 A control-2
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: Cont_3

description:
ST#23 A control-3
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: Monocrotaline-Sedentary replicate 2

description: Library name: 6_4596_29B_S6


title: LpaHI_5_LPS

description: Single RNA


title: Monocrotaline-Sedentary replicate 6

description: Library name: 21_4596_54B_S21


title: Monocrotaline-Sedentary replicate 1

description: Library name: 4_4596_24B_S4


title: LpaHI_2_NT

description: Single RNA


title: MCF_7_4_OHT_4

value: WT


title: MCF_7_4_OHT_3


title: Saline-Exercised replicate 6

description: Library name: 23_4596_59B_S23


title: Saline-Exercised replicate 4

description: Library name: 19_4596_51B_S19


title: LpaHI_1_NT

description: Single RNA


title: MCF_7_4_OHT_1


title: SQ-3_2

city: Beijing

first: Xiangning

last: Liu

address: Chaoyang District, N.3rd Ring Rd East

institute: Beijing University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Rnor_6.0  and  mm10
Supplementary files format and content: tab-delimited text files include raw conuts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Heart

extract_protocol:
mRNA was extracted using trizol
NEB library, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand-specific library, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Heart


title: Saline-Exercised replicate 3

description: Library name: 17_4596_48B_S17


title: Saline-Exercised replicate 5

description: Library name: 20_4596_52B_S20


title: Cont_1

description:
ST#23 A control-1
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt

value: Mouse tumors from KxPxCx injection


title: LpaHI_1_LPS

description: Single RNA


title: MCF_7_DMSO_5


title: PDAC-lung, sample 20, lpWGS [PN6]

city: NY

first: Morteza

last: Chalabi Hajkarim

state: NY

address: 630 West 168th Street

department: Hemo/Onco

institute: CUIMC

description: low pass whole genome sequencing

library_source: genomic

data_processing:
library strategy: lpWGS (low pass whole genome sequencing)
fastq to sam conversion using bowtie2 v2.4.5
sam to bam conversion using samtools v1.16.1
bam to wig conversion using readCounter (hmmcopy_utils)
wig to seg file conversion using ichorCNA v0.2.0
Assembly: hg38
Supplementary files format and content: tumor.cna.seg is cna prediction segmentation file
Supplementary files format and content: tumor.seg is ichorCNA tumor cna prediction segmentation file

molecule: genomic DNA

source_name: pancreas

extract_protocol:
Frozen tissue specimens with edge lengths ranging from 2 to 10 mm were obtained and embedded in optimal cutting temperature (OCT) compound (Tissue-Tek, Sankura; #4583) on dry ice. The specimens were mounted on sample holders and excess OCT was carefully trimmed away, leaving approximately 5 mm of OCT around each side of the tissue nd were mounted on sample holders of a Leica CM1950 cryostat (Leica, Wetzlar, Germany) using a small amount of OCT. Multiple 20 µm tissue curls were cut per tissue using the cryostat and collected in pre-cooled 5 ml tubes (Eppendorf, Hamburg, Germany) to ensure no thawing occurred during transfer. The tissue curls were immediately stored on dry ice until further processing. The number of curls collected depended on the size of the tissue, ranging from 3 to 4 curls for large specimens (1 cm^2) to 10 to 15 curls for core needle biopsies, with the aim of preserving most of the specimens for future investigation. All subsequent steps were performed on wet ice. To extract nuclei, the tubes containing tissue curls were moved from dry ice to wet ice and allowed to briefly equilibrate. After 30 seconds, 5 ml of ice-cold PBS without calcium or magnesium (Thermo Fisher, #10010023) were added to the tubes, and the tubes were inverted until all OCT had dissolved and the clean tissue was collected by centrifugation at 300 x g for 2 min. The tissue was then resuspended in 2 ml of ST buffer [146 mM NaCl, 10 mM Tris-HCL pH 7.5, 1 mM CaCl2, and 21 mM MgCl2 in ultrapure water] containing 0.03% Tween-20 (Sigma Aldrich, #p-7949) and 0.1% BSA (New England Biolabs, B9000S) supplemented with 40 U/mL of RNAse inhibitor (RNAse out, ThermoFisher #10777019). The tissue suspension was thoroughly pipetted 20 times using a 1 ml pipette to mechanically dissociate the tissue and then incubated for 2.5 min on ice. After 2.5 min, the pipetting step was repeated, and the reaction was quenched by adding 4 ml of ST buffer. The sample was filtered through a pre-wetted 70 µm nylon mesh filter (Fisher Scientific) into a 50 ml conical tube. The tube was then centrifuged at 500 x g for 5 min to collect the dissociated nuclei. Following careful decanting of the supernatant, the concentration and quality of the nuclei were determined in a 5 µl aliquot using Neubauer counting chambers (Bulldog Bio, Inc. Portsmouth, NH) and a fluorescent microscope (EVOS FL, Thermo Fisher) after staining of nuclear DNA with 50 µg/ml Hoechst 33342 (Thermo Fisher, H3570).
Excess nuclei (>1x10^5) from the sample preparations for sn-RNAseq were collected by centrifugation (500 x g, 5 min) and snap frozen after removing all but ~10 µL ST buffer and stored until further processing at -20°C. If insufficient numbers of nuclei were available after loading, additional curls were processed using the same methods as described above for single nuclei extraction. To extract genomic DNA from nuclei the nuclei were briefly thawed on wet ice and genomic DNA was extracted using DNAeasy Blood and Tissue kit (Qiagen, Hilden, Germany) according to manufacturer instructions and eluted in RNAse and DNAse free water at 37°C for 5 minutes. The DNA concentration was then quantified using a Nanodrop. 20-50 ng genomic DNA served as input for whole genome sequencing (WGS) library preparation with the Lotus DNA Library Prep Kit (Integrated DNA Technologies - IDT, Coralville, IA) using xGen™ Stubby Adapter (IDT) and UDI Primer Pairs (IDT) according to manufacturer institutions with the following specifications: In the enzymatic preparation program, samples were held at 32°C for 9 minutes. Adapters were not diluted in the ligation step and the optional PCR (5 cycles) and cleanup step were performed so the stubby adapters could be amplified with primers to incorporate the index sequences and P5 and P7 sequences. After library cleanup with AMPure beads (Beckman Coulter, Brea, CA), the libraries were quantified with Qubit 1X dsDNA HS Assay Kit (ThermoFisher) and Tapestation D5000 HS tapes (Agilent) and stored at -20°C until sequencing. The indexed WGS-libraries were mixed and sequenced on an Illumina MiSeq instrument with 1.5X coverage. Furthermore, Bowtie2 v2.5.1 was used to align the fastq files, thereby creating .sam files, which was then converted to .bam and .bai using samtools v1.17. We then generated the read count coverage data using the HMMcopy v1.42.0 R package. This creates a WIG file with 1Mb bins across all chromosomes including reads with a mapping quality greater than 20. This is provided as an input for ichorCNA v0.2.0, generating genome- wide plots representing the log2 ratio copy number for each bin in the genome.

value: pancreas

tag: recurrence site

value: lung

value: TME

tag: neoadjuvant therapy

value: no

tag: lvi

value: yes

tag: pni

tag: tumor location

value: HOP

tag: with snrnaseq


title: MCF_7_4_OHT_2

tag: cell type

tag: treatment


title: PDAC-lung, sample 18, lpWGS [PN4]

description: low pass whole genome sequencing

tag: tissue


title: PDAC-lung, sample 21, lpWGS [PN7]

description: low pass whole genome sequencing


title: SQ-3_3


title: SQ-3_1


title: LQ-40_1


title: LQ-40_3


title: Saline-Exercised replicate 2

description: Library name: 11_4596_37B_S11

value: Rat gastrocnemius muscle


title: Saline-Exercised replicate 1

description: Library name: 7_4596_30B_S7


title: PDAC-lung, sample 17, lpWGS [PN28]

description: low pass whole genome sequencing


title: Saline-Sedentary replicate6

description: Library name: 24_4596_60B_S24


title: MCF_7_DMSO_3


title: LQ-40_2


title: MCF_7_DMSO_2


title: PDAC-lung, sample 15, lpWGS [PN2]

description: low pass whole genome sequencing

value: BOP/TOP


title: Saline-Sedentary replicate5

description: Library name: 22_4596_57B_S22


title: PDAC-lung, sample 16, lpWGS [PN24]

description: low pass whole genome sequencing

value: TOP


title: PDAC-lung, sample 13, lpWGS [PN17]

description: low pass whole genome sequencing


title: MCF_7_DMSO_1


title: Saline-Sedentary replicate2

description: Library name: 13_4596_39B_S13


title: MCF_7_DMSO_4


title: Model3

value: Model


title: Model1


title: Sham3

value: Sham


title: PDAC-lung, sample 10, lpWGS [PN14]

description: low pass whole genome sequencing

value: BOP


title: Female JO, dsxF-/- XX, replicate 2

city: London

first: Joerg

last: Albert

address: 332 Grays Inn Rd

department: Ear Institute

country: United Kingdom

institute: University College London

description:
Library name: Sample 8
Column name in rawCounts.xlsx: DSX_F_JO_S23

data_processing:
Quality control was conducted using MultiQC.
Pseudo-mapping and expression quantification was conducted using Kallisto.
Assembly: Reference transcriptome used (available on vectorbase.org): Anopheles-gambiae-PEST_TRANSCRIPTS_AgamP4.12.fa.gz
Supplementary files format and content: The processed file rawCounts.xlsx is in Excel format; it contains the raw expression counts (following Kallisto quantification) for each transcript in each sample.

organism: Anopheles gambiae

source_name: Johnston's organ

extract_protocol:
RNA was harvested using InvitrogenTM PureLinkTM RNA Mini kit.
RNA libraries for RNA-seq were prepared in accordance with the SMART-Seq v4 Ultra Low Input RNA kit Sequencing User Manual (112219) for Illumina dual-index sequencing.

value: Johnston's organ

value: dsxF-/- XX


title: Female JO, dsxF+/+ XX, replicate 3

description:
Library name: Sample 6
Column name in rawCounts.xlsx: G3_F_JO_S3

value: dsxF+/+ XX


title: Female JO, dsxF-/- XX, replicate 1

description:
Library name: Sample 7
Column name in rawCounts.xlsx: DSX_F_JO_S15


title: Female JO, dsxF-/- XX, replicate 3

description:
Library name: Sample 9
Column name in rawCounts.xlsx: DSX_F_JO_S7


title: Saline-Sedentary replicate4

description: Library name: 16_4596_46B_S16


title: chx10cre_ptbp1_ko3_bulkrna

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: KO3
paired-end fastq files

data_processing:
Bulk RNA-seq: Sequencing results were processed through the rMATS-turbo pipeline which performs alignment with STAR and differential splicing analysis. Gene-level counts were then extracted from the resulting BAM files using featureCounts.
Assembly: mm10
Supplementary files format and content: sample-by-gene count matrix for all the samples as csv

source_name: Retina

extract_protocol:
Retinas were harvested at E16 and RNA was extracted using the TRIzol total RNA extraction protocol.
Illumina Stranded mRNA Prep Ligation kit was used to create the bulk RNA-seq libraries

value: Retina

tag: age

tag: library type

value: mRNA


title: Sham2

value: Heart


title: Female JO, dsxF+/+ XX, replicate 2

description:
Library name: Sample 5
Column name in rawCounts.xlsx: G3_F_JO_S19


title: PDAC-liver, sample 8, lpWGS [PN9]

description: low pass whole genome sequencing

value: pancreas

value: liver


title: chx10cre_ptbp1_ko2_bulkrna

description:
Library name: KO2
paired-end fastq files


title: PDAC-liver, sample 7, lpWGS [PN8]

description: low pass whole genome sequencing

value: TME

value: no


title: chx10cre_ptbp1_ko1_bulkrna

description:
Library name: KO1
paired-end fastq files


title: Male JO, dsxF+/+ XY, replicate 3

description:
Library name: Sample 3
Column name in rawCounts.xlsx: G3_M_JO_S9

value: dsxF+/+ XY


title: Female JO, dsxF+/+ XX, replicate 1

description:
Library name: Sample 4
Column name in rawCounts.xlsx: G3_F_JO_S11


title: Saline-Sedentary replicate3

description: Library name: 15_4596_44B_S15

value: Rat gastrocnemius muscle


title: Alkbh5loxp/loxp; Lyz2-Cre replicate 2 Input

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

description:
Alkbh5cKO_rep2_Input
A5KO_rep2_peaks.narrowPeak.gz

data_processing:
Adaptors removed by trim_galore(0.6.10).
BAM files were generated by alignment to the reference genomic regions using the HISAT2.
PCR replicates were removed using the samtools tool.
MACS3 was used for the callpeak of the m6A peak.
Assembly: mm39
Supplementary files format and content: NarrowPeak format file, the callpeak result of the MACS3

source_name: Bone marrow-derived macrophage

growth_protocol:
1. Mice were sacrificed by CO2 exposure.
2. Clip the skin mid-back and remove the skin from the lower part of the body.
3. Remove tissue from legs with scissors and dissect away from body.
4. Clean remaining tissue from the pelvic and femoral bones and separate at knee joint. Be careful not to break the bones. It is important to make sure that all the tissue is removed from the bones since cells associated with this can contaminate the marrow preparation and potentially overgrow the macrophages.
5. Immerse the bones in 75% ethanol for 5 min, then immerse them in cell medium or PBS for 5 min and leave them in cell medium or PBS until the next step.
6. Cut off each end of bone.
7. Using a 261/2 g needle/10 ml syringe filled with cell medium or PBS; expel the bone marrow from both ends of the bone with a jet of cell medium or PBS directed into a 50 ml cell tube ( until the bone turn white).
8. Centrifuge the cells at 450g for 5min.
9. Discard supernatant, treat cell with 2ml RBC lysis for 4min at room temperature.
10. Add cold cell medium or PBS to RBC lysis up to 15ml.
11. Filter the cell suspension with small filter.
12. Centrifuge at 450g for 5min.
13. Counting cell. (Numbers =4*each area numbers/4× dilution ratio (e.g.12×5 or 10 times ×104))
14. Seed cell at concentration of 5M/well in 6-well-plate with 2-3 ml DMEM culture medium (including 1% glutamate and 1% P/S) with 20% FBS and 30ng/ml M-CSF.
15. Add 2-3 ml medium at 3 or 4 day after seeding.
16. At 7-10 day, the cell were harvested and stained with CD11b and F4/80 (the marker for mature macrophage).
17. Sorting cell for further experiments.

extract_protocol:
To perform MeRIP-seq on BMDMs, start by enriching PolyA RNA from at least 10 µg of total RNA using the DYNABEADS MRNA PURIFICATION Kit (61006) according to the manufacturer's instructions, followed by purification with VAHTS RNA Clean Beads (N412-02) and elution in 10-20 µl of nuclease-free water.
Fragment the eluted RNA at 94°C for 30 seconds using Thermo Fisher Scientific RNA Fragmentation Reagents (AM8740) and purify the fragmented RNA using the ZYMO RNA Clean & Concentrator Kit (R1016). Proceed with the m6A RNA immunoprecipitation (IP) according to the established protocol, ensuring optimal antibody binding and RNA recovery. Following IP, construct the RNA library using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) and purify the library with VAHTS DNA Clean Beads (N411-02). Finally, examine the purified library on a 2% agarose gel, aiming for an ideal library size of approximately 250 bp.

value: Bone marrow-derived macrophage


title: PDAC-lung, sample 11, lpWGS [PN15]

description: low pass whole genome sequencing

value: lung

value: yes

value: HOP


title: PDAC-liver, sample 6, lpWGS [PN3]

description: low pass whole genome sequencing


title: PDAC-liver, sample 5, lpWGS [PN27]

description: low pass whole genome sequencing

value: TOP


title: chx10cre_ptbp1_het2_bulkrna

description:
Library name: HET2
paired-end fastq files


title: Model2

value: Model


title: Male JO, dsxF+/+ XY, replicate 1

description:
Library name: Sample 1
Column name in rawCounts.xlsx: G3_M_JO_S1

value: Johnston's organ


title: Alkbh5loxp/loxp; Lyz2-Cre replicate 1 Input

description:
Alkbh5cKO_rep1_Input
A5KO_rep1_peaks.narrowPeak.gz


title: Mettl3loxp/loxp; Lyz2-Cre replicate 2 IP

description:
Mettl3cKO_rep2_IP
M3KO_rep2_peaks.narrowPeak.gz


title: chx10cre_ptbp1_het1_bulkrna

description:
Library name: HET1
paired-end fastq files


title: chx10cre_bulkrna

description:
Library name: WT
paired-end fastq files


title: Alkbh5loxp/loxp; Lyz2-Cre replicate 1 IP

description:
Alkbh5cKO_rep1_IP
A5KO_rep1_peaks.narrowPeak.gz


title: PDAC-liver, sample 3, lpWGS [PN18]

description: low pass whole genome sequencing


title: PDAC-liver, sample 4, lpWGS [PN23]

description: low pass whole genome sequencing


title: Sham1

value: Sham


title: TRISS042, CD45 CD19 cells, B cells, sTCRseq

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: TRISS042 CD45 CD19 TCR
10x Genomics

library_source: other

data_processing:
Reads from single cells isolated using 10x chromium were demultiplexed and aligned to the GRCh38.p12 human reference genome (from 10x Genomics) using Cell Ranger (version 6.0.1; 10x Genomics).
Assembly: GRCh38.p12
Supplementary files format and content: Tab-separated values files, matrix files and comma-separated values files
Library strategy: TCR-Seq

molecule: other

source_name: Endometrial tumor tissue

extract_protocol:
Tumor tissue from endometrial cancer patients was collected during primary surgery. Tumors were minced into pieces and enzymatically digested with RPMI (Gibco) containing 1 mg/ml Collagenase type IV (Sigma) and 13 U/ml Pulmozyme (Roche), using the GentleMACS Dissociator (Miltenyi), program h_tumor_01.01. Digestion was either done overnight at room temperature or for 30 minutes at 37 °C. Digests were filtered using 70 µm cell strainers and cells were enriched using Ficoll-Paque PLUS (GE Healthcare). After washing with PBS, digests were cryopreserved in fetal bovine/calf serum supplemented with 10% dimethylsulfoxide (DMSO), and stored at liquid nitrogen until use. The day of the experiment, tumor digests were thawed in 2 mL of FCS, centrifuged at 300 g for 5 min, supernatant was discarded, and pellet was resuspended in 0.5 mL of RPMI + 10% FCS. After 1.5h incubation at 37°C/5% CO2, samples were stained and incubated with a CXCR5 PerCP-Cy5.5 antibody for an additional 0.5h at 37°C. After a total of 2h recovery at 37°C/5% CO2, samples were centrifuged and resuspended in 100 µl PBS/2% FCS containing the appropriate surface antibodies. Samples were incubated for 30-45 minutes on ice (in dark) with the following antibodies: CD45-BV605, CD8-APC Cy7, CD4-PE, CD19-BV421, PD1-APC, CD3-PE-Cy7 (Table S1). 3 µl of each antibody was used per 1x10e6 cells. Samples were washed twice with PBS/2% FCS and filtered using a 35 µm strainer (Falcon) before sorting on a Beckman Coulter MoFlo Astrios cytometer. UltraComp eBeads (Thermo Fisher Scientific) were used as compensation controls. Before sorting, Propidium Iodide was added to exclude dead cells. Sorting was done in 1.5 mL Low Bind DNA tubes (Eppendorf) in 150 µl PBS 0.04 % BSA. CD45+ CD3- CD19+ (B cells), CD45+ CD3+ CD19- CD8+ (CD8 cells) and CD4+ (CD4 cells) or CD45+ CD3- CD19- cells were sorted. Sorted cells were centrifuged and resuspended at a concentration of 727 – 2121 cells/µl (total 16.5 µl), in PBS 0.04% BSA, depending on the total number of sorted cells and sample. When the target number of cells from a given population could not be reached for any sample, those cells were jointly loaded onto the chromium chip with cells from the CD3- CD19- CD45 population. As such, the fraction of single cells sequenced does not quantitatively reflect the immune cell composition per sample (Fig S1). Subsequent steps were performed according to manufacturer’s protocol (10x genomics): ‘chromium next GEM single cell 5’ reagents kit v2 (dual index)’. For the cDNA amplification step, 13 cycles were performed according to the manufacturer’s instructions. For each sample, both the V(D)J library as well as the gene expression (GEX) library was constructed. All cDNA quality control and quantification steps were done with the Qubit 4 Fluorometer (Thermo Fisher) and the Agilent 4200 Tapestation (with D5000 and high sensitivity D5000 screen tapes). For the sequencing, V(D)J and GEX libraries were pooled at a 1:4 molar ratio. 1.5 pM of the superpool was sequenced on a NextSeq 500 (Illumina inc., San Diego, 521 CA, USA). A 150 bp NextSeq high-output reagent kit was used for the sequencing (paired end).
Library construction was performed according to manufacturer’s protocol (10x genomics): ‘chromium next GEM single cell 5’ reagents kit v2 (dual index)’. For the cDNA amplification step, 13 cycles were performed according to the manufacturer’s instructions. For each sample, both the V(D)J library as well as the gene expression (GEX) library was constructed. All cDNA quality control and quantification steps were done with the Qubit 4 Fluorometer (Thermo Fisher) and the Agilent 4200 Tapestation (with D5000 and high sensitivity D5000 screen tapes). For the sequencing, V(D)J and GEX libraries were pooled at a 1:4 molar ratio. 1.5 pM of the superpool was sequenced on a NextSeq 500 (Illumina inc., San Diego, 521 CA, USA). A 150 bp NextSeq high-output reagent kit was used for the sequencing (paired end).

treatment_protocol: Patients were treated following standard-of-care health care procedures in the Netherlands for endometrial cancer

value: Endometrial tumor tissue

value: B cell

value: POLE tumor, WT B cells

value: Standard of Care


title: PDAC-liver, sample 2, lpWGS [PN10]

description: low pass whole genome sequencing

value: pancreas

value: liver


title: Saline-Sedentary replicate1

description: Library name: 9_4596_33B_S9


title: Alkbh5loxp/loxp; Lyz2-Cre replicate 2 IP

description:
Alkbh5cKO_rep2_IP
A5KO_rep2_peaks.narrowPeak.gz


title: Mettl3loxp/loxp; Lyz2-Cre replicate 2 Input

description:
Mettl3cKO_rep2_Input
M3KO_rep2_peaks.narrowPeak.gz


title: sn_ATAC_6h_longEE_rep2

city: Boston

first: Erin

middle: Elizabeth

last: Duffy

state: MA

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

description:
Library name: sn_ATAC_6h_longEE_rep2
single nuclei ATAC-seq

library_source: genomic single cell

data_processing:
bulk RNA-seq: Illumina adapters were trimmed with Cutadapt (version 1.14) and aligned using Hisat252 (version 2.1.0) to the Mus musculus genome (GRCm39) and transcriptome (Ensembl). Aligned BAM files were sorted using Picard Tools (version 2.8.0).
snMultiome-seq: Raw sequencing data were processed using Cell Ranger ARC (v2.0.2, 10x Genomics) under default settings. Reads were mapped to mouse mm10 genome, with the GENCODE vm23 GTF file as used in the BICCN atlas.28 We performed unsupervised clustering with RNA UMI counts based on the SCANPY analysis pipeline61 and best practice steps.62,63 In brief, we first filtered for low-quality nuclei by requiring ≥1,000 ATAC fragments and ≥200 genes detected per nuclei and < 5% mitochondria RNA reads. We then performed a first-pass clustering for quality control. Top 3,000 highly variable genes were identified for principal component analysis (PCA). Top 30 PCs were used to perform K-nearest neighbor (k=25) graph-based Leiden clustering (resolution=1). Putative multiplets were predicted using Scrublet64 and Leiden clusters with mean doublets score > 0.2 were marked as doublets. 87-92% cells generated from Cell Ranger ARC for each replicate passed these filtering steps. We then integrated our high-quality cells with hippocampal formation (HPF) cells selected from the whole-mouse brain atlas dataset from BICCN.28 The integration was performed using Seurat's integration methods as previously described.65 We annotated 14 major cell types, and 33 sub-class level cell types based on the integration results as the cell type nomenclature used in this study.
Assembly: bulk RNA-seq: GRCm39; snMultiome-seq: GRCm38
Supplementary files format and content: bulk RNA-seq: aligned, filtered and sorted bam files
Supplementary files format and content: snMultiome-seq: h5ad filtered counts

source_name: hippocampus

growth_protocol: Mice were handled according to protocols approved by the Harvard University Standing Committee on Animal Care and were in accordance with federal guidelines. Wild-type C57/BL6 (JAX 000664) were housed in a 12 h light/dark cycle with ad libitum access to food. For all sequencing studies, male mice were used to avoid the confounding effects of estrogen cycles observed in females

extract_protocol:
Mice were deeply anesthetized with isoflurane, decapitated and brains were placed in a stainless-steel brain matrix on ice to cut 1mm sections of anterior to posterior hippocampus. Sections were transferred into ice-cold PBS and Cornu Ammonis (CA)1, CA3 and Dentate Gyrus (DG) separated under a dissection microscope. Tissue was frozen in liquid nitrogen and stored at -80° for further processing and RNA extraction. For bulk RNA-seq,tissue was resuspended in 500 µL TRIzol reagent (Life Technologies), followed by trituration with a 26G needle. RNA was chloroform extracted, an equal volume of 100% ethanol was added, and RNA was purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction, including the on-column DNase digest.  For single-nuclei multiomic-sequencing whole hippocampi were dissected on an ice-cold metal block and immediately processed for nuclei preparation.
For bulk RNA-seq, RNA concentration was assessed by Nanodrop and RNA-seq libraries were prepared from 10 ng of total RNA using the SMARTer Stranded Total RNA-seq Pico Input Mammalian V2 kit (Takara Bio) according to the manufacturer’s instructions. For snMultiom-seq, freshly dissected hippocampi were dissociated, nuclei were prepared then concentrated in 1X nucleus buffer from 10X Genomics.  1µl of nuclei was stained with Trypan Blue (Invitrogen, T10282) and manually counted. In total, 16,000–20,000 nuclei were used for the tagmentation reaction and 10x Chromium controller loading. The DNA and RNA libraries were generated according to the manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).

treatment_protocol: Adult mice (8-10 weeks of age) were single housed and brought to the room in which behavior was conducted 2-3 nights prior to exposure to novel environment. During this time, mice were housed in a 12 h light/dark cycle with ad libitum access to food. For novel environment stimulation, mice were placed in a square arena (16”x16”) containing a running wheel, tunnel, falcon tubes, Lego pyramid, and a tube rack for 30 min, returned to their home cage, and brain tissue was harvested at indicated times after the start of novel environment (except for 15 and 30 min timepoints for which tissue was harvested without return to homecage). For 6 h continuous novel environment stimulation, mice were placed into the arena containing toys and hydro gel for 6 h. Arena and toys were cleaned prior to experimentation and in between animals with 70% EtOH.    Importantly, tissue was always collected before the animals entered the dark cycle, so the gene expression changes observed are likely not activated in response to changes in response to light state. We collected replicates from the same time point at different times of day to control for gene expression changes driven by circadian rhythms rather than NE exposure. Our initial dataset also included bulk RNA-seq following 12 h of NE exposure, but this time point was later excluded as all mice were harvested at the same time immediately before the dark cycle began and therefore gene expression changes due to NE exposure and circadian rhythms could not be deconvoluted.

value: hippocampus

tag: strain

value: 6 h NE


title: sn_ATAC_1h_EE_rep2

description:
Library name: sn_ATAC_1h_EE_rep2
single nuclei ATAC-seq

value: 30 min NE + 30 min HC


title: PDAC-liver, sample 1, lpWGS [PN1]

description: low pass whole genome sequencing

value: TME

value: no


title: chx10cre_ptbp1_het3_bulkrna

description:
Library name: HET3
paired-end fastq files

value: Retina

value: mRNA


title: Male JO, dsxF+/+ XY, replicate 2

description:
Library name: Sample 2
Column name in rawCounts.xlsx: G3_M_JO_S17

value: dsxF+/+ XY


title: PDAC-lung, sample 20, snRNAseq [PN6]

description:
10x Genomics 5' capture kit
Misc.RData.zip
compartments.RData.zip

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes#v7-0-0)
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 is an h5 (hierarchical data format) file storing three tab-delimited tables for features (genes), barcodes (nuclei) and gene counts output by the 10x Genomics' Cell Ranger pipeline.
Supplementary files format and content: compartments.zip strores RData files for each compartment in the PDAC TME. These files are needed to reproduce the results of the paper.
Supplementary files format and content: Misc.zip strores various data files, such as Milo and ContactTracing outputs, in RData format needed to reproduce the results of the paper.

molecule: nuclear RNA

extract_protocol:
Frozen tissue specimens with edge lengths ranging from 2 to 10 mm were obtained and embedded in optimal cutting temperature (OCT) compound (Tissue-Tek, Sankura; #4583) on dry ice. The specimens were mounted on sample holders and excess OCT was carefully trimmed away, leaving approximately 5 mm of OCT around each side of the tissue nd were mounted on sample holders of a Leica CM1950 cryostat (Leica, Wetzlar, Germany) using a small amount of OCT. Multiple 20 µm tissue curls were cut per tissue using the cryostat and collected in pre-cooled 5 ml tubes (Eppendorf, Hamburg, Germany) to ensure no thawing occurred during transfer. The tissue curls were immediately stored on dry ice until further processing. The number of curls collected depended on the size of the tissue, ranging from 3 to 4 curls for large specimens (1 cm^2) to 10 to 15 curls for core needle biopsies, with the aim of preserving most of the specimens for future investigation. All subsequent steps were performed on wet ice. To extract nuclei, the tubes containing tissue curls were moved from dry ice to wet ice and allowed to briefly equilibrate. After 30 seconds, 5 ml of ice-cold PBS without calcium or magnesium (Thermo Fisher, #10010023) were added to the tubes, and the tubes were inverted until all OCT had dissolved and the clean tissue was collected by centrifugation at 300 x g for 2 min. The tissue was then resuspended in 2 ml of ST buffer [146 mM NaCl, 10 mM Tris-HCL pH 7.5, 1 mM CaCl2, and 21 mM MgCl2 in ultrapure water] containing 0.03% Tween-20 (Sigma Aldrich, #p-7949) and 0.1% BSA (New England Biolabs, B9000S) supplemented with 40 U/mL of RNAse inhibitor (RNAse out, ThermoFisher #10777019). The tissue suspension was thoroughly pipetted 20 times using a 1 ml pipette to mechanically dissociate the tissue and then incubated for 2.5 min on ice. After 2.5 min, the pipetting step was repeated, and the reaction was quenched by adding 4 ml of ST buffer. The sample was filtered through a pre-wetted 70 µm nylon mesh filter (Fisher Scientific) into a 50 ml conical tube. The tube was then centrifuged at 500 x g for 5 min to collect the dissociated nuclei. Following careful decanting of the supernatant, the concentration and quality of the nuclei were determined in a 5 µl aliquot using Neubauer counting chambers (Bulldog Bio, Inc. Portsmouth, NH) and a fluorescent microscope (EVOS FL, Thermo Fisher) after staining of nuclear DNA with 50 µg/ml Hoechst 33342 (Thermo Fisher, H3570).
A total of 0.9-1.4x10^3 nuclei were loaded into ST buffer without RNAse inhibitor using a Chromium controller and chromium reagents (10x genomics) using 5' capture kit. Reverse transcription, cleanup steps, TCR enrichment and final Gene Expression and TCR libraries were performed according to the manufacturer's instructions. To account for the relatively lower amount of RNA in nuclei compared to whole cells, an additional cycle of cDNA amplification was included during library generation. Final libraries were quantified using Tapestation D1000 and D5000 reagents (Agilent) and an Agilent 4150 TapeStation system. Subsequently, the individual libraries were pooled and sequenced on the NovaSeq S4 platform (Illumina, San Diego, CA). The sequencing was designed to target >20,000 reads per cell for gene expression libraries and >5,000 reads per cell for TCR libraries, with a minimum coverage of 2x100 BP (base pairs).

value: lung

value: yes

value: HOP

tag: with lpwgs


title: Mettl3loxp/loxp; Lyz2-Cre replicate 1 IP

description:
Mettl3cKO_rep1_IP
M3KO_rep1_peaks.narrowPeak.gz

value: Bone marrow-derived macrophage


title: sn_ATAC_HC_rep2

description:
Library name: sn_ATAC_HC_rep2
single nuclei ATAC-seq

value: Home cage


title: snRNA_6h_longEE_rep2

description:
Library name: snRNA_6h_longEE_rep2
single nuclei RNA seq


title: TRISS008, CD3 T cells, sTCRseq

description:
Library name: TRISS008 CD3 TCR
10x Genomics

value: Endometrial tumor tissue

value: T cell

value: POLE tumor, WT T cells


title: PDAC-lung, sample 19, snRNAseq [PN5]

value: pancreas

value: TOP


title: WT replicate 2 IP

description:
WT_rep2_IP
WT_rep2_peaks.narrowPeak.gz

value: WT


title: TRISS008, CD45 cells, sTCRseq

description:
Library name: TRISS008 CD45 TCR
10x Genomics

value: CD45 cell

value: POLE tumor, WT CD45 cells

value: Standard of Care


title: WT replicate 2 Input

description:
WT_rep2_Input
WT_rep2_peaks.narrowPeak.gz


title: TRISS042, CD3 T cells, sTCRseq

description:
Library name: TRISS042 CD3 TCR
10x Genomics


title: snRNA_1h_EE_rep2

description:
Library name: snRNA_1h_EE_rep2
single nuclei RNA seq

value: hippocampus

value: 30 min NE + 30 min HC


title: PDAC-lung, sample 18, snRNAseq [PN4]

value: TME

value: no


title: PDAC-lung, sample 17, snRNAseq [PN28]

value: lung

value: yes


title: WT replicate 1 IP

description:
WT_rep1_IP
WT_rep1_peaks.narrowPeak.gz

value: Bone marrow-derived macrophage


title: TRISS001, CD45 cells, sTCRseq

description:
Library name: TRISS001 CD45 TCR
10x Genomics


title: Adult mouse, Pseudomonas treated -3

city: New York

first: Rebecca

middle: F

last: Hough

state: New York

address: 3959 Broadway, CHN 10-24

department: Pediatrics

institute: Columbia University Irving Medical Center

description:
Library name: AP3
Column name in clean_counts: AP3

data_processing:
sequences aligned to GRCm39 mouse genome using STAR aligner
DE analysis done using EdgeR
DE comparison using a generalized linear model (GLM)
Assembly: sequences aligned to GRCm39 mouse genome using STAR aligner
Supplementary files format and content: csv file includes raw counts from each sample

source_name: lung endothelium

extract_protocol:
RNA was extracted using miRNeasy kit (Qiagen). 0.17-1.5 ug of total RNA was used for the construction of sequencing libraries.
Library contruction performed by Genewiz/Azenta

value: lung endothelium

value: Adult mouse

value: freshly isolated lung endothelial cells

value: Pseudomonas


title: PDAC-lung, sample 16, snRNAseq [PN24]

value: pancreas


title: WT replicate 1 Input

description:
WT_rep1_Input
WT_rep1_peaks.narrowPeak.gz


title: PDAC-lung, sample 21, snRNAseq [PN7]

value: HOP


title: TRISS036, CD45 CD19 cells, B cells, sTCRseq

description:
Library name: TRISS036 CD45 CD19 TCR
10x Genomics

value: Endometrial tumor tissue

value: B cell

value: POLE tumor, WT B cells


title: snRNA_HC_rep2

description:
Library name: snRNA_HC_rep2
single nuclei RNA seq

value: Home cage


title: PA14_Plasma_P1

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

country: France

institute: IBS

description:
Library name: PA14-P1
PCR amplicon from gDNA

data_processing:
All analysis performed on usegalaxy.org - Adaptor removal - Trim sequences Galaxy Version 1.0.2+galaxy0 - first base to keep: 34
Drop poor quality reads - Trimmomatic Galaxy Version 0.38.0- sliding widow Number of bases to average across: 4 average
Reads mapping - Bowtie2 Galaxy Version 2.3.4.3+galaxy0
Count aligned reads in features - Ht-seq count Galaxy Version 0.9.1
Differentially represented features - DESeq2 Galaxy Version 2.11.40.6+galaxy1
Assembly: EC2A-CHA: GCF_003698505.1, YIK: JAPTST000000000, UCBPP-PA14: GCF_000014625.1
Supplementary files format and content: Excel file containing DESeq2 results and normalized counts for both analysis of genes and intergenic regions

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol: Mutant library grown at 30°C, incubation in plasma/Heat inactivated plasma for 3h at 37°C on rotating wheel and harvest of live bacteria in LB

extract_protocol: Fragmentation, End repair, DA tailing, adaptor ligation, size selection and 2-step PCRs

treatment_protocol: Plasma vs Heat inactivated plasma (treated at 56°C for 30min to inactivate the complement system)

value: Bacteria

value: Strain PA14

value: Heparinized pooled human plasma (output)


title: PA14_Plasma_P2

description:
Library name: PA14-P2
PCR amplicon from gDNA


title: PDAC-lung, sample 15, snRNAseq [PN2]

value: TME

value: no

value: BOP/TOP


title: Adult mouse, Pseudomonas treated - 2

description:
Library name: AP2
Column name in clean_counts: AP2

value: WT


title: Mettl3loxp/loxp; Lyz2-Cre replicate 1 Input

description:
Mettl3cKO_rep1_Input
M3KO_rep1_peaks.narrowPeak.gz

value: Bone marrow-derived macrophage


title: BCa_R#3

first: mingrui

last: pang

address: Yanjiangxi Road

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Mouse BCa tissue

extract_protocol:
The anti-PD-1 treated BCa tissues were isolated and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Mouse BCa tissue

tag: cell line

value: responsive

tag: Sex

value: female

value: anti-PD-1 antibody


title: PDAC-lung, sample 14, snRNAseq [PN19]

description:
10x Genomics 5' capture kit
Misc.RData.zip
compartments.RData.zip

value: pancreas

value: lung

value: yes

value: TOP


title: TRISS036, CD3 T cells, sTCRseq

description:
Library name: TRISS036 CD3 TCR
10x Genomics

value: Endometrial tumor tissue

value: T cell

tag: genotype

value: POLE tumor, WT T cells

value: Standard of Care


title: PA14_Inactivated-plasma_I1

description:
Library name: PA14-I1
PCR amplicon from gDNA

value: Bacteria

value: Strain PA14

value: Heat inactivated heparinized pooled human plasma (output)


title: Adult mouse, Pseudomonas treated -1

description:
Library name: AP1
Column name in clean_counts: AP1

value: lung endothelium

value: Adult mouse

value: freshly isolated lung endothelial cells

value: WT

value: Pseudomonas


title: BCa_R#1

value: Mouse BCa tissue

value: responsive

value: female

value: anti-PD-1 antibody


title: PA14_Inactivated-plasma_I2

description:
Library name: PA14-I2
PCR amplicon from gDNA


title: Adult mouse, saline control - 3

description:
Library name: AS3
Column name in clean_counts: AS3

value: saline


title: BCa_NR#3

value: non-responsive


title: BCa_R#2


title: PDAC-lung, sample 13, snRNAseq [PN17]

value: pancreas

value: lung

value: TME

value: no

value: yes

value: HOP


title: Adult mouse, saline control -2

description:
Library name: AS2
Column name in clean_counts: AS2

value: lung endothelium


title: PDAC-lung, sample 12, snRNAseq [PN16]


title: YIK_Plasma_P1

description:
Library name: YIK-P1
PCR amplicon from gDNA

value: Bacteria

value: Strain YIK

value: Heparinized pooled human plasma (output)


title: Adult mouse, saline control -1

description:
Library name: AS1
Column name in clean_counts: AS1

value: Adult mouse

value: freshly isolated lung endothelial cells

value: WT


title: PDAC-lung, sample 11, snRNAseq [PN15]


title: YIK_Inactivated-plasma_I2

description:
Library name: YIK-I2
PCR amplicon from gDNA

value: Heat inactivated heparinized pooled human plasma (output)


title: BCa_NR#1

value: Mouse BCa tissue

value: female

value: anti-PD-1 antibody


title: Weanling mouse, Pseudomonas treated -3

description:
Library name: JP3
Column name in clean_counts: JP3

value: Weanling mouse

value: Pseudomonas


title: Astrocytes, shGADD45G-3

city: Dallas

first: tianjin

last: shen

state: Texas

address: 5323 Harry Hines Boulevard, Dallas, TX 75390

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
STAR (v2.5) was applied to align the paired-end clean reads to the mouse reference genome.
HTSeq v0.6.1 was used to count the mapped reads for each gene and the read counts were expressed as fragments per kilobase of exon per million (FPKM).
Differential expression analysis between two groups (three biological replicates per group) was performed using DESeq2 R (2_1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw data for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: astrocytes

growth_protocol: Primary astrocytes were prepared from neonatal cortices of wild-type C57BL/6J at postnatal day 3 and cultured with with astrocyte culture medium (DMEM with 10% FBS and 1% penicillin/streptomycin).

extract_protocol:
Total RNA was harvested using a PureLink RNA Mini Kit.
RNA libraries for RNA-seq were prepared using stranded RNA-seq kits

treatment_protocol: Upon reaching confluency after 8-10 days, astrocytes were purified and subcultured for transduction. After transduction, astrocytes were cultured with serum-free C2 medium (DMEM:F12:Neurobasal (2:2:1), 1% N2 and 1% B27) for 1 week

value: astrocytes

value: GADD45G knockdown

value: no serum culture


title: PDAC-lung, sample 9, snRNAseq [PN13]

value: pancreas

value: lung

value: TME

value: no

value: yes

value: TOP


title: Weanling mouse, Pseudomonas treated - 2

description:
Library name: JP2
Column name in clean_counts: JP2

value: lung endothelium

value: freshly isolated lung endothelial cells


title: PDAC-lung, sample 10, snRNAseq [PN14]

value: BOP


title: YIK_Inactivated-plasma_I1

description:
Library name: YIK-I1
PCR amplicon from gDNA

value: Bacteria

value: Strain YIK

value: Heat inactivated heparinized pooled human plasma (output)


title: CHA_Plasma_P2

description:
Library name: CHA-P2
PCR amplicon from gDNA

value: Strain CHA

value: Heparinized pooled human plasma (output)


title: Astrocytes, shGADD45G-2

value: astrocytes


title: PDAC-liver, sample 8, snRNAseq [PN9]

value: liver

value: HOP


title: YIK_Plasma_P2

description:
Library name: YIK-P2
PCR amplicon from gDNA


title: Astrocytes, shGADD45G-1

value: GADD45G knockdown

value: no serum culture


title: CHA_Plasma_P1

description:
Library name: CHA-P1
PCR amplicon from gDNA


title: PDAC-liver, sample 6, snRNAseq [PN3]

value: pancreas

value: TME


title: PDAC-liver, sample 7, snRNAseq [PN8]

value: no

value: yes


title: Weanling mouse, saline control - 2

description:
Library name: JS2
Column name in clean_counts: JS2

value: lung endothelium

value: Weanling mouse

value: WT

value: saline


title: Astrocytes, shLuc-2

value: shLuc


title: Astrocytes, shLuc-3


title: Weanling mouse, saline control -3

description:
Library name: JS3
Column name in clean_counts: JS3

value: freshly isolated lung endothelial cells


title: CHA_Inactivated-plasma_I2

description:
Library name: CHA-I2
PCR amplicon from gDNA

value: Bacteria

value: Strain CHA

value: Heat inactivated heparinized pooled human plasma (output)


title: CHA_Inactivated-plasma_I1

description:
Library name: CHA-I1
PCR amplicon from gDNA


title: PDAC-liver, sample 5, snRNAseq [PN27]

description:
10x Genomics 5' capture kit
Misc.RData.zip
compartments.RData.zip

value: liver

value: TOP


title: Astrocytes, shLuc-1

value: astrocytes


title: Weanling mouse, saline control - 1

description:
Library name: JS1
Column name in clean_counts: JS1


title: BCa_NR#2

value: Mouse BCa tissue

value: non-responsive

value: female

value: anti-PD-1 antibody


title: sn_ATAC_6h_longEE_rep1

description:
Library name: sn_ATAC_6h_longEE_rep1
single cell multiomics

data_processing:
bulk RNA-seq: Illumina adapters were trimmed with Cutadapt (version 1.14) and aligned using Hisat252 (version 2.1.0) to the Mus musculus genome (GRCm39) and transcriptome (Ensembl). Aligned BAM files were sorted using Picard Tools (version 2.8.0). Reads were quantified over annotated exons using FeatureCounts (Subread version 2.0.6). Lowly expressed genes were filtered for counts per million >1 in at least five samples using edgeR (version 4.0.16).
snMultiome-seq: Raw sequencing data were processed using Cell Ranger ARC (v2.0.2, 10x Genomics) under default settings. Reads were mapped to mouse mm10 genome, with the GENCODE vm23 GTF file as used in the BICCN atlas.28 We performed unsupervised clustering with RNA UMI counts based on the SCANPY analysis pipeline61 and best practice steps.62,63 In brief, we first filtered for low-quality nuclei by requiring ≥1,000 ATAC fragments and ≥200 genes detected per nuclei and < 5% mitochondria RNA reads. We then performed a first-pass clustering for quality control. Top 3,000 highly variable genes were identified for principal component analysis (PCA). Top 30 PCs were used to perform K-nearest neighbor (k=25) graph-based Leiden clustering (resolution=1). Putative multiplets were predicted using Scrublet64 and Leiden clusters with mean doublets score > 0.2 were marked as doublets. 87-92% cells generated from Cell Ranger ARC for each replicate passed these filtering steps. We then integrated our high-quality cells with hippocampal formation (HPF) cells selected from the whole-mouse brain atlas dataset from BICCN.28 The integration was performed using Seurat's integration methods as previously described.65 We annotated 14 major cell types, and 33 sub-class level cell types based on the integration results as the cell type nomenclature used in this study.
Assembly: bulk RNA-seq: GRCm39; snMultiome-seq: GRCm38
Supplementary files format and content: bulk RNA-seq: one table of raw counts, with each column corresponding to a sample, pre-filtered for lowly expressed genes.
Supplementary files format and content: scMultiome: CellRanger count matrix after alignment, filtering, barcode counting, and UMI counting

value: hippocampus

value: 6 h NE


title: Zebrafish Testis scATACseq replicate 2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

description: Library name: Zebrafish_Testis_scATAC_rep2

data_processing:
Data processing with CellRanger ATAC (v.1.2) count pipeline
Assembly: danRer11
Supplementary files format and content: matrices, bed

organism: Danio rerio

source_name: Testis

growth_protocol: Wild Type Adult zebraifsh were used.

extract_protocol:
Adult transgenic zebrafish (Danio rerio), aged six months, were prepared and anesthetized with 0.25% tricaine methanesulfonate (MS-222) on ice for 15 minutes prior to experimentation. Testes samples were dissected from these zebrafish and rinsed three times with PBS. The samples were then digested in 10 ml of 0.25% trypsin at 37°C for 15 minutes, with gentle pipetting every 3 minutes to break down the tissue. The digestion process was stopped using DMEM containing 10% FBS, and the resulting cell suspension was passed through a 70 μm nylon mesh filter. The cells were centrifuged at 1,000 rpm for 10 minutes. After centrifugation, the cells were resuspended in 1 ml of DMEM (with 10% FBS) and subsequently filtered through a 40 μm nylon mesh.
Libraries were constructed using 10X Genomics Chromium Single Cell ATAC (v1.0) kit.

value: Testis

tag: developmental stage

value: Adult


title: Zebrafish Testis scATACseq replicate 1

description: Library name: Zebrafish_Testis_scATAC_rep1


title: Weanling mouse, Pseudomonas treated - 1

description:
Library name: JP1
Column name in clean_counts: JP1

value: lung endothelium

value: Weanling mouse

value: WT

value: Pseudomonas


title: PDAC-liver, sample 3, snRNAseq [PN18]

value: pancreas

tag: recurrence site

value: TME

value: no

value: yes

value: HOP


title: Astrocytes, GADD45G-2

value: astrocytes

value: no serum culture


title: sn_ATAC_1h_EE_rep1

description:
Library name: sn_ATAC_1h_EE_rep1
single cell multiomics

value: 30 min NE + 30 min HC


title: sn_ATAC_HC_rep1

description:
Library name: sn_ATAC_HC_rep1
single cell multiomics

value: Home cage


title: Astrocytes, GADD45G-3


title: PDAC-liver, sample 2, snRNAseq [PN10]

value: liver

tag: neoadjuvant therapy


title: 20201208SV_12

city: Leuven

first: Sophie

last: Vlayen

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven

description:
Library name: Sample 12
T46 DMSO_2
CPM_counts_T46.csv

data_processing:
Sequencing was performed on a HiSeq X (150 bp paired-end reads), and results were analysed using CRISPRCloud2 (CC2). CC2 uses a beta-binomial model with a modified Student’s t-test to determine sgRNA level significance followed by Fisher’s combined probability test to determine gene level significance.
Assembly: GRCh38.96
Supplementary files format and content: csv
Library strategy: CRISPR Screen

source_name: Bone marrow

extract_protocol:
QIAamp DNA Blood Maxi kit (Qiagen) using RNase A (Qiagen)
2-step PCR with Truseq primers and dual index

treatment_protocol: Six cell populations (three replicates of vehicle-treated cells and three replicates of PI-treated cells) were cultured for at least 20 cell doublings in the presence of carfilzomib.

value: Bone marrow

value: Plasma cell

value: DMSO


title: 20201208SV_13

description:
Library name: Sample 13
T46 DMSO_3
CPM_counts_T46.csv


title: PDAC-liver, sample 1, snRNAseq [PN1]

tag: lvi


title: 20201208SV_11

description:
Library name: Sample 11
T46 DMSO_1
CPM_counts_T46.csv


title: Astrocytes, GFP-3

value: GFP


title: snRNA_6h_longEE_rep1

description:
Library name: snRNA_6h_longEE_rep1
single cell multiomics

value: hippocampus

value: 6 h NE


title: Astrocytes, GADD45G-1


title: snRNA_1h_EE_rep1

description:
Library name: snRNA_1h_EE_rep1
single cell multiomics


title: 20201208SV_10

description:
Library name: Sample 10
T46 carfilzomib_3
CPM_counts_T46.csv

value: Carfilzomib


title: snRNA_HC_rep1

description:
Library name: snRNA_HC_rep1
single cell multiomics


title: Astrocytes, GFP-1


title: MCF-7,FOXK1

first: Zhao

middle: Ming

last: hui

address: You'anmen

institute: Capital Medical university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.001
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Breast cancer

tag: chip antibody

value: FOXK1 (Abcam #ab18196)


title: Astrocytes, GFP-2


title: 20201208SV_9

description:
Library name: Sample 9
T46 carfilzomib_2
CPM_counts_T46.csv


title: MCF-7,Input


title: 20201208SV_8

description:
Library name: Sample 8
T46 carfilzomib_1
CPM_counts_T46.csv


title: PDAC-liver, sample 4, snRNAseq [PN23]

description:
10x Genomics 5' capture kit
Misc.RData.zip
compartments.RData.zip

value: pancreas

value: TME

value: no

tag: pni

tag: tumor location

value: TOP


title: S3

city: Nanchang

first: yunfei

last: Luo

address: No. 1 Min De Road

institute: nanchang university

data_processing:
Illumina bcl2fastq software used for basecalling.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: cells were cultured in High Glucose Dulbecco’s Modified Eagle Medium (HDMEM) supplemented with 10% fetal bovine serum(FBS) and 1% penicillin-streptomycin at 37 ℃in a humidified atmosphere of 5% CO2, with medium replaced every 2 days.

extract_protocol:
Total RNA was isolated from cells using Trizol reagents
SMARTer Stranded Total RNA-Seq Kit version 2 (634413; Takara/Clontech) prepared cDNA libraries, and conducted Illumina sequencing after pooling of different libraries according to the requirements of effective concentration and target data volume

treatment_protocol: hepatocytes were seeded into 6-well plates, which were supplemented with serum- and FBS-free HDMEM/Low Glucose Dulbecco’s Modified Eagle Medium (LDMEM) supplemented with the main components (2% knockout-serum, 1 mM b-mercaptoethanol, 2 mM L-glutamine, 1% B-27, 1% N-2, 1% non-essential amino acids, 20 ng/ml bFGF, 20 ng/ml EGF, 100 IU/ml of penicillin/streptomycin)（S0）, and treated with 5-AZA (5 mM; Sigma) for 48 h, followed by TSA(100 nM; Sigma) for 24 h（S1）, 1X ITS (Invitrogen, Carlsbad, CA, USA) plus RA (2 mM; Sigma) for 7 days（S2）, and in FGF- and EGF-free DMEM supplemented with nicotinamide (10 mM; Sigma) for 7 days（S3）

tag: cell type

value: primary mouse hepatocytes

value: step-wise differentiation


title: S2

tag: treatment


title: 20201208SV_7

description:
Library name: Sample 7
T32 DMSO_3
CPM_counts_T32.csv

tag: tissue


title: DG_6h_longEE_rep3

description:
Library name: DG_6h_longEE_rep3
bulk RNA-seq


title: Mammary Gland, WT FVB, Mouse 49901

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

institute: Barbara Ann Karmanos Cancer Institute Wayne State University School of Medicine

data_processing:
The 75 or 150 base pair paired-end reads were mapped to the mm10 mouse reference genome with Rsubread (v2.0.0).
Transcript abundance was determined using featureCounts from the Rsubread package. Transcript abundance was estimated in counts per million (cpm).
Assembly: mm10
Supplementary files format and content: csv file includes gene symbols and gene Entrez IDs and corresponding raw counts for each gene.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted from flash-frozen mammary tumors and normal mammary gland tissues using the RNeasy Mini Kit (QIAGEN). The concentration of the RNA was determined on a NanoDrop spectrophotometer, and the integrity of the RNA was validated using gel electrophoresis.
The RNA expression library construction and next-generation sequencing were performed at the Genomics Core Facility at UNMC (NextSeq 500) and Novogene.

value: Mammary gland

value: Wildtype


title: Mammary Gland, WT FVB, Mouse 49902


title: S0

value: liver


title: DG_6h_longEE_rep1

description:
Library name: DG_6h_longEE_rep1
bulk RNA-seq


title: 20201208SV_5

description:
Library name: Sample 5
T32 DMSO_1
CPM_counts_T32.csv

value: Bone marrow

value: Plasma cell


title: HprtKO_M148_C

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N Orchard St., Fan Lab

department: Metabolism

institute: Morgridge Institute for Research

description:
raw_counts.txt
fpkm.txt

data_processing:
RNA sequencing was performed by Novogene, utilizing Illumina’s Sequencing by Synthesis (SBS) technology.
Quality control was commenced with base recognition using CASAVA, followed by error rate assessment and GC content analysis.
The data were then subjected to stringent filtration, removing adapter contamination, reads with over 10% uncertain nucleotides, and reads where low-quality bases exceeded 50% of the sequence.
Assembly: Post-filtration, the data were aligned to the mm10 mouse genome using the STAR software.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

growth_protocol: RAW 264.7 cells were cultured in RPMI 1640  with 10% dialyzed fetal bovine serum, 25mM HEPES, 2mM glutamine, 1% antibiotics (penicillin, streptomycin) at 37°C and 5% CO2. Hprt Knockouts were generated by CRISPR

extract_protocol:
For RNA collection, cells were washed twice with DPBS and then lysed with RNA STAT 60. Chloroform was used for phase separation. RNA was precipitated with isopropanol, washed with 75% ethanol, and solubilized in DEPC H2O.
mRNA library preparation was performed by Novogene using poly A enrichment

treatment_protocol: To stimulate RAW 264.7 cells, cells were incubated with 50ng/mL LPS and 10ng/mL recombinant mouse IFNγ  for 48h.

value: Hprt Knockout

tag: time stimulated_with_lps+ifny


title: DG_6h_longEE_rep2

description:
Library name: DG_6h_longEE_rep2
bulk RNA-seq

value: hippocampus


title: CA3_6h_longEE_rep4

description:
Library name: CA3_6h_longEE_rep4
bulk RNA-seq

value: 6 h NE


title: S1


title: 20201208SV_6

description:
Library name: Sample 6
T32 DMSO_2
CPM_counts_T32.csv

value: DMSO


title: CA3_6h_longEE_rep3

description:
Library name: CA3_6h_longEE_rep3
bulk RNA-seq


title: subject58_timeN_Homosapiens_RNAseq

city: Kingston

first: Amanda

middle: M

last: Zacharias

state: Ontario

address: 99 University Avenue

country: Canada

institute: Queen's University

description: Library name: 58_N

data_processing:
Raw-sequencing reads were cleaned by BGI using SOAPnuke v1.5.2 with the parameters “-l 15 -q 0.2 -n 0.05”.
Reads were aligned to GENCODE’s primary human reference genome vGRCh38.p13 with Hisat2 v2.2.1 using parameters "--dta --sensitive --no-discordant --no-mixed".
Samtools v1.10 was used to sort resulting BAM files, mark duplicates, index BAM files.
StringTie v2.1.5 assembled aligned reads into transcripts and quantified their abundance using GENCODE’s vGRCh38.p13 comprehensive gene annotation.
IsoformAnalyzeR v1.17.4 in R v4.2.1 assigned a known gene to “novel” transcripts based on their genomic coordinates when possible.
For network analysis, ComBat-seq from sva v3.36.0 adjusted raw and filtered transcript counts for batch effects. DESeq2 v1.26.0 applied the variance stabilizing transformation to these adjusted counts.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: csv file includes raw transcript counts for each Sample
Supplementary files format and content: csv file includes batch-effect adjusted and variance stabilizing transformed transcript counts for each Sample

source_name: Whole peripheral blood

extract_protocol:
Two tubes of blood were collected twice 12 hours apart (7:00-9:00 and 19:00-21:00) by venipuncture in either arm. A 3mL TempusTM Blood RNA tube (Applied Biosystems, Foster City, CA) was used to collect stabilized whole blood RNA. RNA was extracted using Tempus Spin RNA Isolation kits, according to manufacturer’s protocol. RNA integrity (≥7.5) and concentration were assessed prior to library preparation, with globin clearance.
Library preparation was performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). RNA was taken to prepare the reaction system. The globin mRNA was removed by using GLOBINclear™ Whole Blood Globin Reduction Kit-Human (Ambion, USA). Then, the globin mRNA removed RNA samples were denatured at suitable temperature to open the secondary structure, and mRNA was enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, the enriched mRNA was fragmented with fragmentation reaction. Then the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Related, the synthesized double strand cDNA was subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments through a tailing reaction. Then the adaptors were connected to the double stranded cDNA with adaptor ligation reaction. Finally, the library products were amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products were produced via denaturation. The reaction system for circularization was set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library was amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs were loaded into the patterned nanoarray and sequencing reads of PE 150 bases length were generated on G400 platform (BGI-Shenzhen, China).

value: Whole peripheral blood

tag: age

value: male

tag: timepoint

value: N

tag: batch

tag: opioids


title: HprtKO_M0_C

description:
raw_counts.txt
fpkm.txt


title: subject57_timeN_Homosapiens_RNAseq

description: Library name: 57_N

tag: Sex


title: DG_6h_longEE_rep4

description:
Library name: DG_6h_longEE_rep4
bulk RNA-seq

tag: genotype


title: HprtKO_M148_A

description:
raw_counts.txt
fpkm.txt


title: 20201208SV_3

description:
Library name: Sample 3
T32 carfilzomib_2
CPM_counts_T32.csv

tag: cell line

value: Carfilzomib


title: 20201208SV_2

description:
Library name: Sample 2
T32 carfilzomib_1
CPM_counts_T32.csv


title: HprtKO_M0_B

description:
raw_counts.txt
fpkm.txt


title: CA3_6h_longEE_rep2

description:
Library name: CA3_6h_longEE_rep2
bulk RNA-seq


title: subject54_timeN_Homosapiens_RNAseq

description: Library name: 54_N


title: subject56_timeN_Homosapiens_RNAseq

description: Library name: 56_N


title: CA3_6h_longEE_rep1

description:
Library name: CA3_6h_longEE_rep1
bulk RNA-seq


title: 20201208SV_1

description:
Library name: Sample 1
T0


title: WT_M148_C

description:
raw_counts.txt
fpkm.txt

value: Wild-type


title: CA1_6h_longEE_rep4

description:
Library name: CA1_6h_longEE_rep4
bulk RNA-seq


title: HprtKO_M148_B

description:
raw_counts.txt
fpkm.txt


title: 20201208SV_4

description:
Library name: Sample 4
T32 carfilzomib_3
CPM_counts_T32.csv


title: CA1_6h_longEE_rep3

description:
Library name: CA1_6h_longEE_rep3
bulk RNA-seq


title: 20200713SV_15

description:
Library name: Sample 15
T42 DMSO_3
CPM_counts_T42.csv

treatment_protocol: Six cell populations (three replicates of vehicle-treated cells and three replicates of PI-treated cells) were cultured for at least 20 cell doublings in the presence of bortezomib.


title: subject53_timeN_Homosapiens_RNAseq

description: Library name: 53_N


title: 20200713SV_14

description:
Library name: Sample 14
T42 DMSO_2
CPM_counts_T42.csv


title: WT_M148_B

description:
raw_counts.txt
fpkm.txt


title: 20200713SV_13

description:
Library name: Sample 13
T42 DMSO_1
CPM_counts_T42.csv


title: subject52_timeN_Homosapiens_RNAseq

description: Library name: 52_N

value: female


title: CA1_6h_longEE_rep2

description:
Library name: CA1_6h_longEE_rep2
bulk RNA-seq


title: CA1_6h_longEE_rep1

description:
Library name: CA1_6h_longEE_rep1
bulk RNA-seq


title: subject51_timeN_Homosapiens_RNAseq

description: Library name: 51_N


title: 20200713SV_12

description:
Library name: Sample 12
T42 bortezomib_3
CPM_counts_T42.csv

value: Bortezomib


title: 20200713SV_11

description:
Library name: Sample 11
T42 bortezomib_2
CPM_counts_T42.csv


title: subject55_timeN_Homosapiens_RNAseq

description: Library name: 55_N


title: WT_M0_C

description:
raw_counts.txt
fpkm.txt


title: subject50_timeN_Homosapiens_RNAseq

description: Library name: 50_N


title: DG_24h_EE_rep4

description:
Library name: DG_24h_EE_rep4
bulk RNA-seq

value: 30 min NE + 23.5 h HC


title: WT_M0_B

description:
raw_counts.txt
fpkm.txt


title: HprtKO_M0_A

description:
raw_counts.txt
fpkm.txt


title: DG_24h_EE_rep3

description:
Library name: DG_24h_EE_rep3
bulk RNA-seq


title: WT_M0_A

description:
raw_counts.txt
fpkm.txt


title: DG_24h_EE_rep2

description:
Library name: DG_24h_EE_rep2
bulk RNA-seq


title: 20200713SV_10

description:
Library name: Sample 10
T42 bortezomib_1
CPM_counts_T42.csv


title: subject48_timeN_Homosapiens_RNAseq

description: Library name: 48_N


title: 20200713SV_9

description:
Library name: Sample 9
T0C


title: M1_96h_C

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

source_name: Bone-marrow derived macrophage

growth_protocol: Murine bone marrow-derived macrophages (BMDMs) were isolated from wildtype C57BL/6J mice. Bone marrow cells were isolated and differentiated from 6–12-week-old males or females. BMDMs were cultured in RPMI 1640  with 10% dialyzed fetal bovine serum, 25mM HEPES, 2mM glutamine, 1% antibiotics (penicillin, streptomycin) and 20ng/mL M-CSF at 37°C and 5% CO2.

treatment_protocol: To stimulate BMDMs, cells were incubated with 50ng/mL LPS and 30ng/mL recombinant mouse IFNγ  for 2h. Stimuli then were removed, cells were washed with DPBS, and cell culture was continued in fresh media without stimuli for the remaining timecourse.

value: Bone-marrow derived macrophage

value: 96h later


title: DG_24h_EE_rep1

description:
Library name: DG_24h_EE_rep1
bulk RNA-seq


title: subject47_timeN_Homosapiens_RNAseq

description: Library name: 47_N


title: WT_M148_A

description:
raw_counts.txt
fpkm.txt


title: DG_18h_EE_rep4

description:
Library name: DG_18h_EE_rep4
bulk RNA-seq

value: 30 min NE + 17.5 h HC


title: M1_96h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: 20200713SV_8

description:
Library name: Sample 8
T0B

value: Bone marrow


title: subject46_timeN_Homosapiens_RNAseq

description: Library name: 46_N


title: 20200713SV_7

description:
Library name: Sample 7
T28 DMSO_3
CPM_counts_T28.csv

value: Plasma cell


title: M1_96h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_18h_EE_rep3

description:
Library name: DG_18h_EE_rep3
bulk RNA-seq


title: 20200713SV_6

description:
Library name: Sample 6
T28 DMSO_2
CPM_counts_T28.csv


title: subject45_timeN_Homosapiens_RNAseq

description: Library name: 45_N


title: 20200713SV_5

description:
Library name: Sample 5
T28 DMSO_1
CPM_counts_T28.csv


title: M1_48h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

value: 48h later


title: subject44_timeN_Homosapiens_RNAseq

description: Library name: 44_N


title: DG_18h_EE_rep1

description:
Library name: DG_18h_EE_rep1
bulk RNA-seq

value: hippocampus


title: subject49_timeN_Homosapiens_RNAseq

description: Library name: 49_N


title: M1_48h_C

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_18h_EE_rep2

description:
Library name: DG_18h_EE_rep2
bulk RNA-seq


title: subject43_timeN_Homosapiens_RNAseq

description: Library name: 43_N


title: DG_8h_EE_rep4

description:
Library name: DG_8h_EE_rep4
bulk RNA-seq

value: 30 min NE + 7.5 h HC


title: 20200713SV_3

description:
Library name: Sample 3
T28 bortezomib_2
CPM_counts_T28.csv


title: subject16_batch2_timeN_Homosapiens_RNAseq

description: Library name: 16_N_batch2


title: subject42_timeN_Homosapiens_RNAseq

description: Library name: 42_N


title: M1_24h_C

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

value: 24h later


title: DG_8h_EE_rep3

description:
Library name: DG_8h_EE_rep3
bulk RNA-seq


title: M1_48h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: subject41_timeN_Homosapiens_RNAseq

description: Library name: 41_N

value: Whole peripheral blood


title: DG_8h_EE_rep2

description:
Library name: DG_8h_EE_rep2
bulk RNA-seq


title: M1_24h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: 20200713SV_1

description:
Library name: Sample 1
T0A


title: 20200713SV_2

description:
Library name: Sample 2
T28 bortezomib_1
CPM_counts_T28.csv


title: DG_8h_EE_rep1

description:
Library name: DG_8h_EE_rep1
bulk RNA-seq


title: CF

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

description: Library name: CRN00219817

data_processing:
Raw sequencing data were aligned to the Drosophila melanogaster reference genome (BDGP6.32, Ensembl release 104) using 10x Genomics Cell Ranger v7.1.0.
Low quality nuclei with less than 500 Unique Molecular Identifiers (UMI) were filtered out. The default clustering and uniform manifold approximation and projection (UMAP) generated by 10X Loupe Browser was used to cluster cells.
Cell types were manually annotated using the top marker genes from each cluster.
The filtered count matrix and metadata were loaded into R (v4.4.0) and further processing was performed using the default Seurat workflow (v5.2.1).
Assembly: BDGP6.32
Supplementary files format and content: seurat object, raw read counts

organism: Drosophila melanogaster

source_name: gut

growth_protocol: Oregon R flies were raised at 23C at standard lab food and conditions and 3days old females were collected for the experiment

extract_protocol:
Single-nucleus suspension was conducted as described by Li et 2022. Briefly 70 guts per sample were dissected in cold Schneider’s medium, flash-frozen and stored at -80°C. Prior to FACs sorting, samples were spined down and Schneider’s medium was exchanged with homogenization buffer (Li et 2022). Using 1ml dounce , nuclei were released by 20 loose pestle strokes and 40 tight pestle strokes while keeping samples on ice and avoiding foam. Next, nuclei were filtered through 5 ml cell strainer (40 μm), and using 40 μm Flowmi. Nuclei were centrifuged,  resuspended in PBS/BSA with 0.5% RNase inhibitor and filtered again with 40 μm Flowmi. Single nuclei were sorted using Sony SH800Z Cell Sorter and 100k nuclei per sample were collected in PBS/BSA buffer.
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1

treatment_protocol: For the Recovery sample (A2)  flies were fed with 2%DSS in standard lab food for 4 days  and then transferred to standard lab food for 2 days prior to dissection. For Homeostasis sample (A1) flies were fed with standard lab food for 6 days prior to dissection. Both feeding regimes were conducted at 29C

value: gut

value: mutant, CFTR RNAi knockdown


title: subject40_timeN_Homosapiens_RNAseq

description: Library name: 40_N

value: male

value: N


title: M1_12h_C

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

value: Wild-type

value: 12h later


title: M1_24h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: 20200713SV_4

description:
Library name: Sample 4
T28 bortezomib_3
CPM_counts_T28.csv

value: Bortezomib


title: subject39_timeN_Homosapiens_RNAseq

description: Library name: 39_N

value: female


title: WT

description: Library name: CRN00219816

value: wild type


title: M1_12h_B

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt

value: Bone-marrow derived macrophage


title: DG_6h_EE_rep3

description:
Library name: DG_6h_EE_rep3
bulk RNA-seq

value: 30 min NE + 5.5 h HC


title: M1_12h_A

description:
raw_counts_BMDM.txt
fpkm_BMDM.txt


title: DG_6h_EE_rep2

description:
Library name: DG_6h_EE_rep2
bulk RNA-seq


title: subject38_timeN_Homosapiens_RNAseq

description: Library name: 38_N


title: subject37_timeN_Homosapiens_RNAseq

description: Library name: 37_N


title: spoki, myo1a-EcRi,biorep3

city: Heidelberg

first: Yao

last: Zhang

address: Im Neuenheimer Feld 580

country: Germany

institute: Deutsches Krebsforschungszentrum (DKFZ)

description: Library name: EcRi3

data_processing:
CLC Genomics Workbench
Assembly: dm6
Supplementary files format and content: Feature counts for each sample

source_name: intestine

extract_protocol:
Total RNA were extracted using Qiagen RNeasy mini plus kit
SMARTER mRNA-seq library prep kit was used

value: intestine

value: EcRi