title: Bu-S4

city: Los Angeles

first: Benjamin

last: Macadangdang

address: 10833 Le Conte Ave, MDCC B2-375

institute: University of California, Los Angeles

data_processing:
Raw sequencing reads from RNA-seq experiments were quality filtered and trimmed with fastp v0.23.4121 with default parameters, then mapped to the reference genome of each respective species with bwa-mem2122 with default parameters. Mapping statistics were generated with bamtools123 v2.5.1 and visualized with multiqc124 v1.21. Reads in gene features were counted with featureCounts125 function of the subread package at the fragment level (--countReadPairs) with fragments overlapping multiple features counted in both (-O).
Assembly: GCF_000154125.1, GCF_000210835.1, GCF_000304195.1, GCF_000011065.1, GCF_000154205.1
Supplementary files format and content: tab delimited file of raw counts for each gene

organism: Bacteroides uniformis ATCC 8492

source_name: ATCC 8492

growth_protocol: Bacteroides strains were grown in Brain Heart Infusion (BHI, BD Difco) medium at 37°C, supplemented with vitamin K (5 µg/mL) and hemin (5 µg/mL), and incubated in an anaerobic chamber (Coy) under 5% H2, 10% CO2, 85% N2 for 24 hours.

extract_protocol:
Cells were flash-frozen in a dry ice-ethanol slurry, then pelleted by centrifugation at 16,000xg for 1 minute at 4°C. The bacterial pellets were stored at −80°C until RNA extraction. RNA was extracted using TRIzol reagent and the PureLink™ RNA Mini Kit following the manufacturer’s instructions. Briefly, bacterial pellets were incubated with 1 mL of TRIzol for 5 minutes at room temperature, followed by the addition of 200 µL of chloroform. After 5 minutes at room temperature, the samples were centrifuged at 12,000xg for 15 minutes at 4°C. The aqueous phase was transferred to a new tube, and an equal volume of 100% ethanol was added. This mixture was transferred to a spin cartridge and centrifuged at 12,000xg for 15 seconds at room temperature. RNA samples were treated with PureLink™ DNase I, according to the manufacturer’s protocol. Following DNase treatment and four wash steps, RNA was eluted in 50 µL of RNase-free water by centrifugation at 12,000xg for 1 minute. Eluted RNA was transferred to RNase-free tubes and analyzed for quality by agarose gel electrophoresis. RNA integrity was assessed using the Bio-Rad ChemiDoc system, and RNA concentration was quantified with a NanoDrop One spectrophotometer (Thermo Fisher Scientific). Further RNA quality and concentration was validated on an Agilent 4200 TapeStation RNA ScreenTape, with all RIN scores above 8.0 and samples normalized to 250 ng starting mass.
Library preparation was performed using Illumina’s Stranded Total RNA Prep with Ribo-Zero Plus Microbiome, which targets depletion of microbiome rRNA prior to cDNA synthesis and library formation. Final libraries were validated using an Agilent 4200 TapeStation D1000 ScreenTape, with an average fragment size of 396bp. Libraries were quantified using Invitrogen’s Quant iT High Sensitivity dsDNA Kit and normalized during pooling.

value: ATCC 8492


title: SA-WT3P2

status: Public on Oct 10 2025

type: SRA

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

description: single-stranded RNA, tri-phopshorylated TAATACGACTCACTATAGGAAACTAAAAGGGAGAAGTGAAAGTG and CACTTTCACTTCTCCCTTTTAGTTTCCTATAGTGAGTCGTATTA

library_source: transcriptomic

data_processing:
Reads were first trimmed of adapters and low-complexity sequences with cutadapt 1.14 (-O 5 -f fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT)
Trimmed reads were then sorted with fastq-tools (fastq-sort)
Trimmed reads were mapped against RepBase with STAR v2.4.0j to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (hg19) using STAR aligner (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
featureCounts was used to count reads according to gencode v19 annotations (-s 2 -M)
Assembly: hg19
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: counts text files contain output from featureCounts

molecule: total RNA

organism: Homo sapiens

source_name: human embryonic kidney

growth_protocol: 1X Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2

extract_protocol:
poly(A) selection
Illumina stranded mRNA, part# 15031047 Revision E

treatment_protocol: 2.5 μL Lipofectamine 2000 and 125 μL Opti-MEM medium were combined with a mixture of 1 μg RNA (either ssRNA or 3p-RNA) and 125 μL Opti-MEM per well of a 6-well plate. After 5 min at room temperature, the solution was added drop-wise to cells grown to 70-90% confluence in 2 mL DMEM

tag: tissue

value: human embryonic kidney

tag: cell line

tag: cell type

value: embryonic kidney

tag: genotype

value: wildtype

tag: treatment

value: transfection


title: Mouse_liver_8-weeks-old

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

description:
Library name: 8wks
10X Genomics

library_source: transcriptomic single cell

data_processing:
The initial preprocessing of the data, including mapping against the Mus musculus GRCm39 reference genome and gene counting, was done using the CeleSCOPE software (v2.0.7) (https://singleron.bio/products/celescope/) with the chemistry scopeV3.0.1 (kit V2) and setting the expected number of cells to 60k (--expected_cell_num 60000). The resulting data were imported into R and analyzed with the Seurat package (v5.0.1).
All samples were merged into a single object and processed to remove cells with a low sequencing quality, those with a feature count below 200 and above 6,000, as well as cells with a fraction of mitochondrial genes higher than 5%.
Assembly: GRCm39
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample

organism: Mus musculus

source_name: whole liver

extract_protocol:
Liver samples from 3 mice per age (2 and 8 weeks old) were collected on ice. Single nuclei suspension was obtained from the livers by Singleron Biotechnologies and then equally pooled into a single sample for each age group to be processed for single nuclei RNA sequencing.
cDNA library preparation was performed by Singleron Biotechnologies and 150 bp paired-end reads Illumina sequencing was performed by Macrogen.

value: whole liver

tag: age


title: Bu-S3

tag: strain

value: WT


title: DU145_R1881E_Rep1

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

description: Library name: Sample 7

data_processing:
Raw sequencing data were trimmed using trimmomatic v0.39
Quality of trimmed reads was analyzed using FastQC (v0.12.1)
Qc results were merged using MultiQC (v1.23)
Assembly: Reads were pseudo-aligned to the human reference genome GRCh38 using Kallisto (v0.46.1).
Supplementary files format and content: Raw counts and normalized counts were generated using DESeq2 (v.1.42.1).

growth_protocol: VCaP (CVCL_2235) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% L-glutamine, 1 mM sodium pyruvate;  LAPC4 (CVCL_4744) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% L-glutamine; DU145 (CVCL_0105) were maintained in EMEM supplemented as above and with 1% MEM Non-essential amino acid, 1 mM sodium pyruvate. All cells were maintained at 37°C with 5% CO₂ and cultured for a maximum of four months.

extract_protocol:
Total RNA was extracted with a RNEasy plus mini kit (Qiagen, Toronto, ON, Canada). RNA quantification and quality control were done with a NanoDrop spectrophotometer and Agilent 2100 BioAnalyzer , respectively. Samples had an RNA Integrity Number ≥ 9.5.
RNA sequencing libraries were prepared using NEBNext Ultra II Directional RNA library with NEBNext Poly(A) mRNA (New England Biolabs, Whitby, ON, Canada)

treatment_protocol: Cells were hormone-deprived for 72 hours in phenol-red free medium supplemented with 2% charcoal-stripped serum (CSS). Cells were then treated with 10 nM of an androgen or vehicle only (containing 0.05 % DMSO), with or without 10 µM enzalutamide

value: Prostate cancer CRPC model

value: AR negative

value: R1881 10 nM + enzalutamide 10 uM)

tag: time


title: BMDM, Alpk1-/-, PBS, replicate 3

city: Beijing

first: Yuanhanyu

last: Luo

state: Beijing

address: No.7, Science Park Road, Zhongguancun Life Science Park, Beijing

country: China

institute: National Institute of Biological Sciences

description:
Library name: Sample9
Column name in BMDM_raw_count.csv: KO-NC-9_R1_001

data_processing:
Raw reads were quality-checked using FastQC
Adapter trimming was done with Trim Galore using default parameters.
Clean reads were aligned to the mm10/hg38 genome using STAR
Read counts were generated using featureCounts package.TPM quantification was performed using RSEM.
Differential expression analysis was conducted using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Primary Mouse bone marrow derived macrophages(BMDMs)

extract_protocol:
RNA was extracted using the Vazyme RNA extraction kit (RC112-01) and protocols.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation kit (20040534), following manufacturer's protocols.

treatment_protocol: Cells were treated with 100 μM ALPK1 agonist (ADP-Hep) or PBS for 4 h.

value: Macrophage

value: Alpk1 knockout

value: PBS

value: 4 h


title: DU145_R1881_Rep3

description: Library name: Sample 6


title: Mouse_liver_2-weeks-old

description:
Library name: 2wks
10X Genomics


title: Rat ovarian tissue, PM2.5 exposure 3, 30 days

city: Changchun

first: Zhenhua

last: Ma

state: Jilin

address: Xincheng Street

department: College of Veterinary Medicine

institute: Jilin Agricultural University

description: Library name: PM 3

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). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ensemblv107
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ovary

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.
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. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: ovary

value: Cowshed PM2.5 exposure


title: Bu-S1


title: SA-KOSS1

description: single-stranded RNA, unphosphorylated CACUUUCACUUCUCCCUUUUAGUUUCC

value: PARP13 knockout, homozygous


title: DU145_R1881_Rep1

description: Library name: Sample 4


title: DU145_11KT_Rep1

description: Library name: Sample 10

value: 11KT 10 nM


title: Bu-S2

value: ATCC 8492


title: Bo-S4

organism: Bacteroides ovatus ATCC 8483

source_name: ATCC 8483

value: ATCC 8483


title: BMDM, Alpk1-/-, PBS, replicate 1

description:
Library name: Sample7
Column name in BMDM_raw_count.csv: KO-NC-7_R1_001

value: Primary Mouse bone marrow derived macrophages(BMDMs)


title: BMDM, WT, ADP-Hep, replicate 3

description:
Library name: Sample6
Column name in BMDM_raw_count.csv: WT-A-6_R1_001

value: ADP-Hep


title: DU145_DMSO_Rep2

description: Library name: Sample 2

value: DMSO


title: Rat ovarian tissue, PM2.5 exposure 1, 30 days

description: Library name: PM 1

value: WT


title: Bo-S3


title: Rat ovarian tissue, control 3, 30 days

description: Library name: control 3


title: BMDM, WT, ADP-Hep, replicate 2

description:
Library name: Sample5
Column name in BMDM_raw_count.csv: WT-A-5_R1_001


title: BMDM, WT, ADP-Hep, replicate 1

description:
Library name: Sample4
Column name in BMDM_raw_count.csv: WT-A-4_R1_001


title: BMDM, Alpk1-/-, ADP-Hep, replicate 1

description:
Library name: Sample10
Column name in BMDM_raw_count.csv: KO-A-10_R1_001


title: DU145_DMSO_Rep1

description: Library name: Sample 1

value: Prostate cancer CRPC model


title: Bo-S2


title: Rat ovarian tissue, control 2, 30 days

description: Library name: control 2


title: Bo-S1


title: Healthy control, distal, sample 6

city: Chicago

first: Matthew

last: Dapas

address: 240 E Huron St

department: Medicine

institute: Northwestern University

description:
Library name: HC6-D
10X Genomics

data_processing:
Sequenced reads were processed using the 10X Genomics Cell Ranger v6.1.2 pipeline and aligned to the GRCh38 transcriptome
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix table of unique molecular index (UMI) counts per gene per sample (filtered for cells over background)
Supplementary files format and content: matrix table of unique molecular index (UMI) counts per gene per sample (unfiltered)

molecule: polyA RNA

source_name: Esophageal mucosa

extract_protocol:
During endoscopy, esophageal mucosal biopsies were obtained at approximately 5-cm (“distal esophagus”) and 15-cm (“proximal esophagus”) from the squamocolumnar junction using Boston Scientific Radial Jaw 4 standard capacity forceps. Tissue samples were subjected to mechanical and chemical digestion. Cell suspensions were processed for encapsulation using a Chromium iX controller (10X Genomics) on a Chromium Next GEM Chip G (10X Genomics).
Cell barcoding and library construction were performed using the 10X Genomics Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 and Dual Index Kit TT Set A

value: Esophageal mucosa

tag: condition

value: healthy control

tag: Sex

value: female

tag: location

value: distal


title: Rat ovarian tissue, control 1, 30 days

description: Library name: control 1


title: BMDM, Alpk1-/-, PBS, replicate 2

description:
Library name: Sample8
Column name in BMDM_raw_count.csv: KO-NC-8_R1_001

value: Macrophage

value: Alpk1 knockout

value: PBS


title: Salmonella Typhimurium D23580 cells, replicant C, after 30mins bicarbonate treatment

city: Liverpool

first: Lijuan

address: University of Liverpool

country: United Kingdom

institute: University of Liverpool

description:
Library name: Sample 12
D23580.annotated.counts.xlsx

data_processing:
Sequencing adapters were removed and reads were demultiplexed by the instrument software (Illumina bcl2fastq v2.20). Gene-level count matrices were generated using featureCounts against GCA_000188735.1 for ST4/74 and GCA_900538085.1 for D23580. . The resulting processed files (474.annotated.counts.xlsx and D23580.annotated.counts.xlsx) are provided as study-level supplementary files covering all samples.
Assembly: GCA_000188735.1 for ST4/74 and GCA_900538085.1 for D23580.
Supplementary files format and content: 474.annotated.counts.xlsx ; D23580.annotated.counts.xlsx

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial cell

growth_protocol: Cells were grew until OD600=2.0, then centrifugated to get cell pellets

extract_protocol:
RNA was extracted using TRIzol kit.
Libraries were constructed by SeqCenter (Pittsburgh, PA, USA) using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit according to the manufacturer’s protocol. rRNA was depleted prior to fragmentation, cDNA synthesis, adapter ligation, and PCR amplification. Sequencing was performed on an Illumina NovaSeq 6000.

treatment_protocol: One group was extracted RNA directly, the other group was treated was bicarbonate (0.53g/30ml) for 30min and  then extracted RNA.

value: wildtype

value: bacterial cell

value: bicarbonate (0.53g/30ml)


title: Healthy control, proximal, sample 6

description:
Library name: HC6-P
10X Genomics

value: proximal


title: Rat ovarian tissue, PM2.5 exposure 2, 30 days

description: Library name: PM 2

value: ovary

value: Cowshed PM2.5 exposure


title: Salmonella Typhimurium D23580 cells, replicant B, after 30mins bicarbonate treatment

description:
Library name: Sample 11
D23580.annotated.counts.xlsx


title: Healthy control, distal, sample 5

description:
Library name: HC5-D
10X Genomics


title: DU145_DMSO_Rep3

description: Library name: Sample 3

value: AR negative


title: Salmonella Typhimurium D23580 cells, replicant A, after 30mins bicarbonate treatment

description:
Library name: Sample 10
D23580.annotated.counts.xlsx


title: colon carcinoma MC38 cells and Keap1 wild-type BMDM spheroids, day 5, sample 1

city: Zurich

first: Florence

last: Vallelian

address: Rämistrasse 100

country: Switzerland

institute: University Hospital Zürich

description: Library name: KeapWT1_day5

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.2.0)
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: .h5 output of CellRangerMulti (7.2.0)
Supplementary files format and content: .h5ad containing analyzed data of all samples

source_name: MC38 (tumor cells)

growth_protocol: Multispheroid culture in microwell plates: GFP-MC38 cells + BMDMs (at a 1:1 ratio) were seeded in tumor cell medium with M-CSF in a 24-well SphericalPlate® 5D microwell. Fresh culture cell medium was added on day 3.

extract_protocol:
Spheroid digestion: Spheroids were dissociated in 2 ml digestion medium (RPMI medium (Gibco) + 25 µg/ml Liberase ™ (Roche) + 40 µg/ml DNase I (Roche; 2000 U/ml) and incubated for 30-45 min in a water bath at 37°C with gentle shaking every 5 min. Then, 4 ml PBS + 0.04% BSA was added to stop the digestion.
Single-cell suspensions were fixed following the demonstrated protocol Fixation of cells & Nuclei for Chromium Fixed RNA Profiling (10X Genomics, CG000478) and processed for long-term storage at -80°C. After storage, up to 2 Mio cells per sample were hybridized with unique single Mouse WTA probes using BC001-004 according to the demonstrated protocol Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10X Genomics, CG000527).

value: MC38 (tumor cells)

value: Keap1 wild-type (BMDMs)


title: BMDM, WT, PBS, replicate 3

description:
Library name: Sample3
Column name in BMDM_raw_count.csv: WT-NC-3_R1_001

value: Primary Mouse bone marrow derived macrophages(BMDMs)

value: WT

value: 4 h


title: colon carcinoma MC38 cells and Keap1 knockout BMDM spheroids, day 5

description: Library name: KeapKO_day5

value: Keap1 knockout (BMDMs)


title: Healthy control, distal, sample 4

description:
Library name: HC4-D
10X Genomics

value: Esophageal mucosa

value: healthy control

value: female

value: distal


title: Salmonella Typhimurium D23580 cells, replicant C, before bicarbonate treatment

description:
Library name: Sample 9
D23580.annotated.counts.xlsx

value: wildtype

value: no treatment


title: BMDM, WT, PBS, replicate 1

description:
Library name: Sample1
Column name in BMDM_raw_count.csv: WT-NC-1_R1_001

value: Macrophage

value: PBS


title: colon carcinoma MC38 cells and Keap1 wild-type BMDM spheroids, day 1, sample 2

description: Library name: KeapWT2_day1


title: Healthy control, proximal, sample 4

description:
Library name: HC4-P
10X Genomics

value: proximal


title: Bfine-S3

organism: Bacteroides finegoldii CL09T03C10


title: colon carcinoma MC38 cells and Keap1 wild-type BMDM spheroids, day 1, sample 1

description: Library name: KeapWT1_day1


title: DU145_R1881_Rep2

description: Library name: Sample 5

value: Prostate cancer CRPC model


title: Bfine-S2


title: Healthy control, distal, sample 3

description:
Library name: HC3-D
10X Genomics


title: Bfine-S1


title: Salmonella Typhimurium D23580 cells, replicant A, before bicarbonate treatment

description:
Library name: Sample 7
D23580.annotated.counts.xlsx

value: bacterial cell


title: colon carcinoma MC38 cells and Keap1 knockout BMDM spheroids, day 1

description: Library name: KeapKO_day1

value: MC38 (tumor cells)


title: BMDM, WT, PBS, replicate 2

description:
Library name: Sample2
Column name in BMDM_raw_count.csv: WT-NC-2_R1_001


title: Salmonella Typhimurium 4/74 cells, replicant C, after 30mins bicarbonate treatment

description:
Library name: Sample 6
474.annotated.counts.xlsx

value: bicarbonate (0.53g/30ml)


title: Healthy control, proximal, sample 3

description:
Library name: HC3-P
10X Genomics


title: Bfrag-S4

organism: Bacteroides fragilis 638R


title: colon carcinoma MC38 cells and Keap1 wild-type BMDM spheroids, day 5, sample 2

description: Library name: KeapWT2_day5

value: Keap1 wild-type (BMDMs)


title: Healthy control, distal, sample 2

description:
Library name: HC2-D
10X Genomics


title: Salmonella Typhimurium 4/74 cells, replicant B, after 30mins bicarbonate treatment

description:
Library name: Sample 5
474.annotated.counts.xlsx


title: 7209 LE

city: St. Louis

first: Liang

state: MO

address: 660 S. Euclid Ave

department: Medicine, Obstetrics and Gynecology

institute: Washington University

description:
Library name: Sample 5
sample.7209.uterine.le

data_processing:
RNA-seq reads were aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR1 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma2. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights3.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: tab-delimited text files includes raw transcript counts for each sample

source_name: Uterine luminal epithelium

growth_protocol: Female mice were considered 0.5 days post-coitum (dpc) pregnant upon observation of vaginal plubs after mating. 3.5dpc pregnancy timepoint was confirmed by presence of blastocysts upon PBS flush of uterine horns. 4.5dpc pregnancy timepoint was confirmed by presence of implantation sites during Chicago blue tail vein injection procedure.

extract_protocol:
Uterine luminal epithelium was isolated by cutting horns into ~4mm segments, opening segments longitudinally to form sheets, shaking sheets in 1mL 1% w/v trypsin in calcium and magnesium free HBSS in 15mL conical tubes for 1.5hr at 4C o a shaking platform, followed by  30 min. shaking at room temperature. 4mL additional HBSS was added to each tube and tubes were shaken vigorously by hand to encourage LE sheets to detach. Contents of each tube was poured onto a 6cm dish. The large chunks were removed with tweezers and placed in new tube for subsequent stromal processing. HBSS was collected from the dish by pipetting and spun at 9,000xG for 5 minutes. Supernatant was removed and remaining pellet was considered isolated LE. To isolate uterine stroma, remaining uterine chunks were incubated in 1mL 0.25% trypsin with 1mg/mL collagenase in HBSS at 37C on a platform shaker at 200rpm for 30 minutes. 3mL additional HBSS was then added to eachy tube, and 5mL serological pipette was used to pipette up and down at least 25 times to release the stromal cells into solution. This was then again moved to a 6cm petri dish, and large chunks (serous and muscle layers) were removed with tweezers and discarded. Remaining solution was passed through a 100um nylon filter (cell strainer), strainer was rinsed with 1mL full serum hESC growth media, and solution was transferred to tubes and spun at 9,000xG for 5 minutes. Pellets were washed once with 500uL full serum hESC growth media to inhibit remaining trypsin, and solutions were spun again at 9,000xG for 5 minutes. Supernatant was removed and remaining pellet was considered isolated uterine stroma. Uterine luminal epithelia and stroma was washed with cold PBS and RNA was isolated using Qiagen RNeasy kit with Dnase treatment.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Uterine luminal epithelium

value: Sall1 fl/fl

value: pregnancy 3.5dpc

tag: batch

value: seq request 4/27/22


title: Bfrag-S3

value: WT


title: Healthy control, proximal, sample 5

description:
Library name: HC5-P
10X Genomics

value: Esophageal mucosa

value: healthy control

value: female


title: Bfine-S4


title: Low dose infection 12 hours

city: Harbin

first: xinyang

last: zhang

address: 678 Haping Road, Xiangfang District, Harbin City, Heilongjiang Province

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the official software Cell Ranger from 10×Genomics.
Assembly: GRCm39
Supplementary files format and content: Tap-separated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood was collected from the orbital vein into EDTA anticoagulant tubes at each time point, and the blood samples were gently inverted to ensure thorough mixing with the anticoagulant. Approximately 300-400 µL of blood was collected from each mouse, with samples from 5 mice per time point pooled together in a new anticoagulant tube for subsequent extraction of peripheral blood mononuclear cells.Transfer 4 ml of density gradient centrifugation fluid into a density gradient centrifugation tube and allow it to equilibrate to room temperature. Carefully add 1 ml of blood sample slowly onto the top layer of the centrifugation fluid using a pipette. Then, initiate centrifugation without braking mode at 400 x g for 30 minutes. After centrifugation, gently aspirate the PBMC layer cells into a new 15 ml centrifuge tube and add 9 ml of serum-free RPMI1640 culture medium for washing, followed by centrifugation at 250 x g for 10 minutes. Discard the supernatant, add 1 ml of red blood cell lysis reagent to each tube, and incubate for 5 minutes. Then, add 9 ml of RPMI1640 culture medium, mix well, and centrifuge at 250 x g for 10 minutes. Discard the supernatant, add 2 ml of RPMI1640 to resuspend the pellet, and filter through a sieve to remove cell clumps. Add another 3 ml of RPMI1640 to wash the original tube and filter again. Transfer 5 ml of PBMC suspension to a new 15 ml centrifuge tube and centrifuge at 250 x g for 10 minutes. Discard the supernatant and resuspend the cells in 500 μl of PBS containing 1% BSA to obtain mouse peripheral blood mononuclear cells (PBMCs).
The single-cell RNA-Seq libraries were prepared using the Chromium™ Single Cell 3' Solution kit from 10×Genomics. In brief, single-cell suspensions were combined with a mixture containing gel beads encapsulating Barcode information, Unique Molecular Identifier (UMI) information, Poly(dT)VN capture sequences, and primers, and then entered into a microfluidic device where they were encapsulated in oil droplets, forming the Gel Beads-In-Emulsions (GEMs). Subsequently, the gel beads inside the GEMs were dissolved, releasing the 3’-end mRNA sequences captured by Poly(dT)VN, which were reverse transcribed to generate cDNA molecules tagged with Barcodes and UMIs for sequencing. After disrupting the emulsion, a cDNA amplification reaction was performed, followed by purification, quality assessment, and enzymatic fragmentation of the qualified cDNA samples. The 3' ends of the fragmented cDNA were blunt-ended and adenylated. Additionally, P5 and P7 adapter sequences were ligated to the 5' and 3' ends of the fragments, respectively. Subsequently, target-sized fragments were selected and recovered, followed by quality control and quantification of the sequencing libraries. Finally, the prepared libraries were subjected to high-throughput sequencing using the Illumina sequencing platform with paired-end 150-base pair reads.

value: Blood

value: PBMC

value: BALB/c

value: 6-8 weeks old


title: Healthy Control


title: Bfrag-S2


title: Salmonella Typhimurium 4/74 cells, replicant C, before bicarbonate treatment

description:
Library name: Sample 3
474.annotated.counts.xlsx

value: wildtype

value: no treatment


title: Low dose infection 8 hours


title: Healthy control, distal, sample 1

description:
Library name: HC1-D
10X Genomics

value: distal


title: Salmonella Typhimurium 4/74 cells, replicant A, after 30mins bicarbonate treatment

description:
Library name: Sample 4
474.annotated.counts.xlsx

value: bacterial cell

value: bicarbonate (0.53g/30ml)


title: Salmonella Typhimurium 4/74 cells, replicant B, before bicarbonate treatment

description:
Library name: Sample 2
474.annotated.counts.xlsx


title: Low dose infection 4 hours


title: Healthy control, proximal, sample 2

description:
Library name: HC2-P
10X Genomics

value: proximal


title: Healthy control, proximal, sample 1

description:
Library name: HC1-P
10X Genomics


title: Low dose infection 2 hours


title: DSD5

first: Yisa

last: Wang

address: 1035 Boshuo Rd., Nanguan District

institute: Changchun University of Chinese Medicine

description: Iso-RNA(ONT)

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for Iso-RNA(ONT) were prepared using EXP-FLP001 PRO.6 following manufacturer's protocols

value: lung


title: Salmonella Typhimurium 4/74 cells, replicant A, before bicarbonate treatment

description:
Library name: Sample 1
474.annotated.counts.xlsx


title: DSD4

description: Iso-RNA(ONT)


title: Muscle, control, replicate5

first: Luzi

last: Yang

address: 38 Xueyuan Road, Haidian District

institute: Peking University Health Science Ce

library_source: genomic

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a NNNNNNNNNNNNNN(private) \ -g NNNNNNNNNNNNNNNNNNNNN(Private) \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table

molecule: genomic DNA

source_name: Muscle

extract_protocol:
Genomic DNA was extracted from tissues using TIANamp Genomic DNA Kit (DP304, Tiangen, China)
The sgRNA-targeted loci were amplified using Taq PCR MasterMix (KT211, Tiangen, China) and purified by TIANgel Purification Kit (DP219, TIANGEN).
Amplicon-seq

value: Muscle

value: Control


title: DSD3

description: Iso-RNA(ONT)

value: WT


title: High dose infection 2 hours


title: GERD, distal, sample 3

description:
Library name: GERD3-D
10X Genomics

value: Esophageal mucosa

value: GERD


title: DSD2

description: Iso-RNA(ONT)


title: GERD, distal, sample 4

description:
Library name: GERD4-D
10X Genomics

value: female


title: Brain, control, replicate5

source_name: Brain

value: Brain


title: Td9_A12,Cre

library_source: other

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom  perl and python scripts.
Clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data.
Q20, Q30, and GC-content of the raw data were calculated.
The gene counting and aggregation were made using the python program (small_rna_seq2count.py).
Assembly: mm10
Supplementary files format and content: Counts_Small_RNA_Seq.txt

molecule: other

source_name: liver

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEB Next® Multiplex Small RNA  Library Prep Set for Illumina® （NEB E7300L）. Briefly, 3’ and 5’ adaptors  were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand  cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment.  After purification and size selection, libraries with insertions between18~40 bp  were ready for sequencing on Illumina sequencing with SE50. Subsequently, library quality was assessed on the Agilent 5400 system （Agilent，USA）and quantified by QPCR（1.5nM）. The Qualified libraries were  pooled and sequenced on Illumina platforms with SE50 strategy in Novogene  Bioinformatics Technology Co., Ltd (Beijing, China), according to effective  library concentration and data amount required.

value: liver


title: GERD, proximal, sample 3

description:
Library name: GERD3-P
10X Genomics


title: DSD1

description: Iso-RNA(ONT)


title: Bfrag-S1


title: Td9_A11,Cre


title: GERD, distal, sample 2

description:
Library name: GERD2-D
10X Genomics


title: Lung, control, replicate5

source_name: Lung

value: Lung


title: Kindey, control, replicate5

source_name: Kindey

value: Kindey


title: CLP5

description: Iso-RNA(ONT)


title: Salmonella Typhimurium D23580 cells, replicant B, before bicarbonate treatment

description:
Library name: Sample 8
D23580.annotated.counts.xlsx

value: wildtype


title: GERD, proximal, sample 2

description:
Library name: GERD2-P
10X Genomics


title: Td9_A10,Cre


title: Liver, control, replicate5

source_name: Liver

value: Liver


title: CLP4

description: Iso-RNA(ONT)


title: Spleen, control, replicate5

source_name: Spleen

value: Spleen


title: Td9_A4,Cre-miR122


title: Scleroderma, distal, sample 10

description:
Library name: SSc10-D
10X Genomics

value: scleroderma

value: distal


title: CLP3

description: Iso-RNA(ONT)


title: High dose infection 6 hours

value: Blood

value: PBMC

value: BALB/c

value: 6-8 weeks old


title: Heart, control, replicate5

source_name: Heart

value: Heart

value: WT

value: Control


title: GERD, proximal, sample 4

description:
Library name: GERD4-P
10X Genomics

value: Esophageal mucosa

value: GERD

value: female

value: proximal


title: Td9_A1,Cre-miR122

value: liver


title: CLP2

description: Iso-RNA(ONT)

value: lung


title: Muscle, control, replicate4

value: Muscle


title: Scleroderma, proximal, sample 9

description:
Library name: SSc9-P
10X Genomics


title: Kindey, control, replicate4

value: Kindey


title: COM_3

first: Tianxiao

last: Xu

address: 52 Fucheng Road, Haidian District, Beijing

institute: Peking University Cancer Hospital

data_processing:
Clean reads were obtained and stored in FASTQ format after the sequencing data was filtered with SOAPnuke (v1.5.2). HISAT2 was used to map the clean reads to the reference genome (v2.0.4). Then, to detect fusion genes and differential splicing genes (DSGs), Ericscript (v0.5.5) and rMATS (V3.2.5) were utilized. Bowtie2 (v2.2.5) was used to align clean reads to the gene set, a database cre- ated by BGI (Beijing Genomic Institute in ShenZhen) that comprised known and new, coding and noncoding transcripts, and then RSEM was used to calculate gene expression levels (v1.2.12).
Assembly: grch38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: Prostate cell line

value: AgNPs+DOC


title: Scleroderma, distal, sample 8

description:
Library name: SSc8-D
10X Genomics

value: scleroderma

value: distal


title: CLP1

description: Iso-RNA(ONT)


title: COM_2


title: Scleroderma, proximal, sample 8

description:
Library name: SSc8-P
10X Genomics


title: Sham5

description: Iso-RNA(ONT)


title: Lung, control, replicate4

value: Lung


title: Spleen, control, replicate4

value: Spleen


title: Scleroderma, distal, sample 7

description:
Library name: SSc7-D
10X Genomics

value: male


title: Liver, control, replicate4

value: Liver

value: WT


title: DOC_3

value: DOC


title: Scleroderma, proximal, sample 7

description:
Library name: SSc7-P
10X Genomics

value: Esophageal mucosa


title: Scleroderma, distal, sample 6

description:
Library name: SSc6-D
10X Genomics

value: female


title: DOC_2


title: Heart, control, replicate4

value: Heart

value: Control


title: Scleroderma, distal, sample 9

description:
Library name: SSc9-D
10X Genomics


title: Sham1

description: Iso-RNA(ONT)

value: lung


title: Scleroderma, proximal, sample 6

description:
Library name: SSc6-P
10X Genomics

value: proximal


title: Td9_A2,Cre-miR122

value: liver


title: Muscle, control, replicate3

value: Muscle


title: DOC_1

value: Prostate cell line


title: COM_1

value: AgNPs+DOC


title: Scleroderma, distal, sample 5

description:
Library name: SSc5-D
10X Genomics

value: scleroderma

value: distal


title: RPMI-8226, ADU-S100, 10 μM

description:
Library name: Sample26
Column name in raw_counts_All_Samples.csv: S0416-B14

growth_protocol: Cells were cultured in Gibco RPMI 1640, supplemented with 10% fetal bovine serum (FBS), and 1% penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the Vazyme RNA extraction kit (RC112-01) and protocols.
RNA libraries for RNA-seq were prepared using VAHTS mRNA Capture Beads (N401) and VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605-02 (Vazyme) following manufacturer's protocols.

treatment_protocol: Cells were treated with ALPK1 agonist (ADP-Hep or UDSP-Hep), TLR7/8 agonist (R848), or STING agonist (ADU-S100) at the indicated doses for 4 h.

value: B lymphocyte

value: 4 h


title: Brain, control, replicate3

value: Brain


title: RPMI-8226, ADU-S100, 1 μM

description:
Library name: Sample25
Column name in raw_counts_All_Samples.csv: S0416-B13

value: ADU-S100, 1 μM


title: AgNPs_3

value: WT

value: AgNPs


title: Kindey, control, replicate3

value: Kindey


title: Scleroderma, proximal, sample 5

description:
Library name: SSc5-P
10X Genomics

value: Esophageal mucosa

value: female


title: RPMI-8226, ADU-S100, 0.1 μM

description:
Library name: Sample24
Column name in raw_counts_All_Samples.csv: S0416-B12


title: Sham2

description: Iso-RNA(ONT)

value: lung


title: AgNPs_2


title: Sham4

description: Iso-RNA(ONT)


title: Scleroderma, distal, sample 4

description:
Library name: SSc4-D
10X Genomics


title: RPMI-8226, R848, 10 μM

description:
Library name: Sample23
Column name in raw_counts_All_Samples.csv: S0401-B10


title: Lung, control, replicate3

value: Lung

value: Control


title: Scleroderma, proximal, sample 4

description:
Library name: SSc4-P
10X Genomics

value: proximal


title: AgNPs_1

value: Prostate cell line


title: Spleen, control, replicate3

value: Spleen


title: RPMI-8226, R848, 1 μM

description:
Library name: Sample22
Column name in raw_counts_All_Samples.csv: S0401-B9


title: BLANK_2

value: PBS


title: Scleroderma, distal, sample 3

description:
Library name: SSc3-D
10X Genomics

value: scleroderma

value: distal


title: Liver, control, replicate3

value: Liver


title: RPMI-8226, R848, 0.1 μM

description:
Library name: Sample21
Column name in raw_counts_All_Samples.csv: S0401-B8

value: B lymphocyte

value: 4 h


title: Heart, control, replicate3

value: Heart

value: WT


title: Scleroderma, proximal, sample 3

description:
Library name: SSc3-P
10X Genomics


title: RPMI-8226, UDSP-Hep, 10 μM

description:
Library name: Sample20
Column name in raw_counts_All_Samples.csv: S0401-B7

value: UDSP-Hep, 10 μM


title: BLANK_1


title: L2D2

type: RNA

data_processing:
Data processing was performed by using the internal software of the merscope platform.
cell_by_gene.csv: This file contains a matrix where rows represent individual cells, and columns represent genes. Each entry in the matrix indicates the expression level of a specific gene in a specific cell.
cell_metadata.csv: This file contains metadata for each cell, such as cell type, sample ID, experimental condition, and spatial coordinates within the sample.
detected_transcripts.csv: This file lists the transcripts detected in the experiment, often providing details such as the gene name, transcript count, and spatial location of each detected transcript.
cell_boundaries.parquet: This file contains the spatial boundaries of each cell in the sample, stored in a Parquet format, which is efficient for large datasets. It includes information about the shape and position of each cell’s boundary in the tissue.

extract_protocol: Livers were collected and snap frozen in isopentane, then embedded in Killik OCT on dry ice. For MERFISH  spatial transcriptomic analysis 10-µm slices were cut using Leica cryostat CM1860 and put on commercial Vizgen MERFISH slides. Samples were fixed 30 minutes at 47°C in PFA 4%, washed 3x 5 minutes with PBS, and incubated overnight with EtOH 70% at 4°C. Tissue verification (MERSCOPE Sample Verification kit, human, Vizgen) was performed before MERFISH following the manufacturer’s instructions.

value: liver


title: Muscle, control, replicate2

value: Muscle


title: Scleroderma, distal, sample 2

description:
Library name: SSc2-D
10X Genomics

value: Esophageal mucosa

value: female


title: RPMI-8226, UDSP-Hep, 1 μM

description:
Library name: Sample19
Column name in raw_counts_All_Samples.csv: S0401-B6

value: UDSP-Hep, 1 μM


title: Scleroderma, proximal, sample 2

description:
Library name: SSc2-P
10X Genomics

value: proximal


title: Brain, control, replicate2

value: Brain

value: Control


title: L2D1


title: RPMI-8226, UDSP-Hep, 0.1 μM

description:
Library name: Sample18
Column name in raw_counts_All_Samples.csv: S0401-B5

value: UDSP-Hep, 0.1 μM


title: Scleroderma, distal, sample 1

description:
Library name: SSc1-D
10X Genomics

value: scleroderma

value: male


title: BMDM WT

description: Library name: WT

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.2.0)
Downstream analysis with scanpy 1.9.2
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: .h5 output of CellRangerMulti (7.2.0)

source_name: BMDM

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). For the GM-CSF-supplemented cultures, fresh medium containing recombinant mouse GM-CSF (2×, 40 ng/ml)(PeproTech) was added on day 2. On day 3, half of the medium was removed and new medium supplemented with GM-CSF (20 ng/ml) was added.

extract_protocol:
The BM cells were harvested for analysis on day 5 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.
Single-cell suspensions were fixed following the demonstrated protocol Fixation of cells & Nuclei for Chromium Fixed RNA Profiling (10X Genomics, CG000478) and processed for long-term storage at -80°C. After storage, up to 2 Mio cells per sample were hybridized with unique single Mouse WTA probes using BC001-004 according to the demonstrated protocol Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10X Genomics, CG000527).

value: BMDM

value: wild-type

value: GM-CSF for 5 days


title: BLANK_3

value: Prostate cell line

value: PBS


title: BMDM Nrf2 KO

description: Library name: Nrf2KO

value: Nrf2 knockout


title: Scleroderma, proximal, sample 1

description:
Library name: SSc1-P
10X Genomics


title: Kindey, control, replicate2

value: Kindey

value: WT


title: RPMI-8226, ADP-Hep, 10 μM

description:
Library name: Sample17
Column name in raw_counts_All_Samples.csv: S0401-B4

value: B lymphocyte

value: ADP-Hep, 10 μM

value: 4 h


title: Lung, control, replicate2

value: Lung


title: RPMI-8226, ADP-Hep, 1 μM

description:
Library name: Sample16
Column name in raw_counts_All_Samples.csv: S0401-B3

value: ADP-Hep, 1 μM


title: IGF4

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

description:
Library name: IGF4
125a

data_processing:
QC was perforned using fastQC
Samples were subsampled to 75 millon reads and trimmed to 100nt using seqtk and cutadapt
Reads were aligned to the Hg38 version of the reference genome using STAR v2.7.4a
Quantification of known genomic features was done using featureCounts
Data was normalised with noisyR
Assembly: Hg38
Supplementary files format and content: Raw count matrices, in csv format

source_name: Kidney biopsy

growth_protocol: Samples were stored in RNAlater

extract_protocol:
RNA was extracted from RNAlater stored kidney tissue biopsies using Qiagen RNeasy Midi kit.
rRNA depletion sequencing library was prepared by using Qiagen FastSelect rRNA HMR Kit. Libraries were produced using NEBNext Ultra II RNA Library Preparation Kit for Illumina.

value: Kidney biopsy

tag: sample group

value: IGF


title: Spleen, control, replicate2

value: Spleen

value: Control


title: RPMI-8226, ADP-Hep, 0.1 μM

description:
Library name: Sample15
Column name in raw_counts_All_Samples.csv: S0401-B2

value: ADP-Hep, 0.1 μM


title: Liver, control, replicate2

value: Liver


title: MC38 tumor at 7 days post–irradiation

description: Library name: 7d

data_processing:
Read alignment using SpaceRanger (3.0.1)
Downstream analysis with scanpy 1.9.2
Assembly: GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: *.tar: output of spaceranger
Supplementary files format and content: *.tif: H&E images
Library strategy: Spatial Transcriptomics

source_name: tumor

growth_protocol: Once confluent, GFP-MC38 tumor cells were harvested using 5 mM EDTA (Gibco) (4 min at 37°C). MC38 cells (2 x 106) in culture medium were mixed with Geltrex (Thermo Fisher) and injected subcutaneously into the mouse flanks.

extract_protocol:
Mice were euthanized, and tumors were collected at defined timepoints after irradiation (24h or 7d).
Microtome sections on regular glass slides were deparaffinized and stained for H&E as described by 10X Genomics. Regions of interest on the tissue sections were chosen using H&E staining and aligned in the tissue slide cassette 6.5 mm. After destaining and decrosslinking, sections were immediately subjected to probe hybridization overnight followed by probe ligation, release and extension and spatial library construction as described in the user guide Visium HD Spatial Gene Expression Reagents Kits. Ready-made libraries were sequenced at the Functional Genomics Center Zurich (FGCZ) using paired end 150 bp read configuration.

treatment_protocol: Tumors were irradiated with 12 Gy.

value: tumor

value: MC38 tumor cells

value: irradiation with 12Gy


title: IGF3

description:
Library name: IGF3
122a


title: RPMI-8226, PBS

description:
Library name: Sample14
Column name in raw_counts_All_Samples.csv: S0401-B1

value: PBS


title: Heart, control, replicate2

value: Heart


title: IGF2

description:
Library name: IGF2
102a


title: THP-1, ADU-S100, 10 μM

description:
Library name: Sample13
Column name in raw_counts_All_Samples.csv: S0416-A14

value: Monocyte


title: sample 2

description: Library name: sample_2

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.2.0)
Downstream analysis using scanpy 1.9.2
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: .h5 output of CellRangerMulti (7.2.0)

source_name: sorted macrophages

growth_protocol: Tumor growth model in mice: Once confluent, GFP-MC38 tumor cells were harvested using 5 mM EDTA (Gibco) (4 min at 37°C). MC38 cells (2 x 106) in culture medium were mixed with Geltrex (Thermo Fisher) and injected subcutaneously into the mouse flanks. Agonistic anti-CD40 treatment (20 mg/kg, InVivoPlus, clone FGK4.5) or an isotype control antibody was administered intravenously according to treatment protocol. Mice were euthanized, and tumors were collected at defined timepoints after antibody administration. Tumors were then digested or fixed in formalin (10%) and stored at room temperature.

extract_protocol:
Subcutaneous tumors were excised and minced using a scalpel on a sterile Petri dish. The minced tumor tissue was then dissociated in 3 ml of digestion medium (RPMI medium (Gibco) supplemented with 25 µg/ml Liberase™ (Roche) and 40 µg/ml DNase I (Roche; 2000 U/ml)). This mixture was incubated for 30-45 minutes in a water bath at 37°C, with gentle shaking every 5 minutes. The dissociated tumor cells were filtered through a 70 µm cell sieve and washed with PBS containing 2 mM EDTA to halt the digestion process. Following the lysis of red blood cells using RBC lysis buffer (Biolegend), the cells were washed again and immediately utilized. Cell sorting was performed on a BD FACSAria III 4L.
Single-cell suspensions were fixed following the demonstrated protocol Fixation of cells & Nuclei for Chromium Fixed RNA Profiling (10X Genomics, CG000478) and processed for long-term storage at -80°C. After storage, up to 2 Mio cells per sample were hybridized with unique single Mouse WTA probes using BC001-004 according to the demonstrated protocol Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10X Genomics, CG000527).

value: sorted macrophages

value: Ms4a3-Cre Rosa26-tdTomato


title: IGF1

description:
Library name: IGF1
109a


title: sample 1

description: Library name: sample_1


title: Brain, control, replicate1

value: Brain

value: WT


title: PDGF3

description:
Library name: PDGF3
116a

value: PDGF


title: PDGF2

description:
Library name: PDGF2
121a

value: Kidney biopsy


title: Kindey, control, replicate1

value: Kindey


title: THP-1, R848, 10 μM

description:
Library name: Sample10
Column name in raw_counts_All_Samples.csv: S0401-A10

value: 4 h


title: MC38 tumors treated intravenously (i.v.) with agonistic anti-CD40 on  days 11, 13, and 15 (3xCD40)

description: Library name: 3xCD40

value: C57BL/6 mice

value: MC38 tumors treated intravenously (i.v.) with agonistic anti-CD40 on  days 11, 13, and 15 (multiple injections, 3xCD40)


title: Lung, control, replicate1

value: Lung

value: Control


title: PDGF1

description:
Library name: PDGF1
60a


title: THP-1, R848, 1 μM

description:
Library name: Sample9
Column name in raw_counts_All_Samples.csv: S0401-A9


title: MC38 tumors treated intravenously (i.v.) with agonistic anti-CD40 on day 11 (1xCD40)

description: Library name: 1xCD40

value: MC38 tumors treated intravenously (i.v.) with agonistic anti-CD40 on day 11 (single injection; 1xCD40)


title: MC38 tumors treated intravenously (i.v.) with isotype control (ctrl) on day 11

description: Library name: ctrl


title: Sham3

description: Iso-RNA(ONT)

value: lung


title: THP-1, R848, 0.1 μM

description:
Library name: Sample8
Column name in raw_counts_All_Samples.csv: S0401-A8


title: Spleen, control, replicate1

value: Spleen


title: mouse MC38 tumor treated with aCD40

description: Library name: B23_1556_SM0296

data_processing:
Read alignment using SpaceRanger (3.0.1)
Downstream analysis with scanpy 1.9.2
Assembly: GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: *.tar: output of spaceranger
Supplementary files format and content: *.h5ad: processed sample
Library strategy: Spatial Transcriptomics

growth_protocol: Tumor growth model in mice: Once confluent, GFP-MC38 tumor cells were harvested using 5 mM EDTA and washed twice in PBS. MC38 cells in culture medium were mixed with Geltrex and injected subcutaneously into the mouse flanks. Agonistic anti-CD40 treatment or an isotype control antibody was administered intravenously according to treatment protocol.  Mice were euthanized, and tumors were collected at defined timepoints after antibody administration. Tumors were then fixed in formalin (10%) and stored at room temperature.

extract_protocol:
Organ fixation for paraffin embedding and microtome sectioning: Mice were anesthetized by intraperitoneal injection of ketamine , xylazine , and acepromazine and transcardially perfused with cold PBS. Organs were placed in 10% formalin and transferred in 70% ethanol after 24 hours before embedding in paraffin blocks. Microtome sections (2-2.5 µm) of each organ were cut for H&E staining and immunohistochemistry staining.
Microtome sections on regular glass slides were deparaffinized and stained for H&E as described by 10X Genomics. Regions of interest on the tissue sections were chosen using H&E staining and aligned in the tissue slide cassette 6.5 mm. After destaining and decrosslinking, sections were immediately subjected to probe hybridization overnight followed by probe ligation, release and extension and spatial library construction as described in the user guide Visium HD Spatial Gene Expression Reagents Kits. Ready-made libraries were sequenced at the Functional Genomics Center Zurich (FGCZ) using paired end 150 bp read configuration.

value: tumor

value: MC38 (tumor cells)

value: Nrf2 fl wild-type

value: agonistic aCD40 treatment


title: sh-NT-IP

city: guangzhou

first: Ze

last: Yuan

state: guangdong

address: yuancun

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description: sh-NT-IP

data_processing:
For RNA-seq： Cutadapt (v2.5) was used to trim adapters and filter for sequences. Reads were aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3). Differential gene expression analysis was performed using the DESeq2 R-package.
For m7G MeRIP-seq: Adapter sequences were trimmed from all raw reads using Cutadapt software (version 2.5). The clean sequences were then aligned to the human reference genome(hg38) using Hisat2 software(version 2.1.0) in single-end mode. Samtools software(v1.10) was used to retain only uniquely mapped sequences with a mapping quality score >30. Differential m7G peak were identified using exomePeak R package under parameters:"PEAK_CUTOFF_PVALUE=NA,PEAK_CUTOFF_FDR=0.05,FRAGMENT_LENGTH=200". GO and KEGG analysis were performed using clusterprofile R package (v3.6.0). m7G-RNA-related genomic features were visualized using Guitar R package (v1.16.0). Identified m7G peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 10 -rna”.
Assembly: the human Ensemble genome GRCh38
Supplementary files format and content: DLD1-S-CAFsw13VSDLD1-W13CM.All.fpkm.anno.xls
Supplementary files format and content: DLD1-METTL1-sh2DLD1-METTL1-sh-NT_de_m7G_exp.xls

growth_protocol: The cell lines cultured in this study were maintained in DMEM supplemented with 10% FBS (Gibco; 10%, v/v) and 1% penicillin-streptomycin at 37°C under a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent. 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

treatment_protocol: For RNA-seq, DLD1 cells co-cultured with S-CAFs, DLD1 cells co-cultured with CAFs. For m7G MeRIP-seq, DLD1 cells following METTL1 knockdown.

value: control


title: sh-NT-Input

description: sh-NT-Input


title: THP-1, UDSP-Hep, 10 μM

description:
Library name: Sample7
Column name in raw_counts_All_Samples.csv: S0401-A7

data_processing:
Raw reads were quality-checked using FastQC
Adapter trimming was done with Trim Galore using default parameters.
Clean reads were aligned to the mm10/hg38 genome using STAR
Read counts were generated using featureCounts package.TPM quantification was performed using RSEM.
Differential expression analysis was conducted using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

value: Monocyte

value: UDSP-Hep, 10 μM


title: colon carcinoma MC38 tumor from Keap1 wild-type mouse 2

description: Library name: KeapWT_tumor_2

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.2.0)
Filtering, concatenation, normalization and log(x+1) transformation
dimensionality reduction, clustering
cell type annotation
differential gene expression, scoring of gene sets
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: .h5 output of CellRangerMulti (7.2.0)
Supplementary files format and content: .h5ad containing analyzed data of all samples

growth_protocol: Tumor growth model in mice: Once confluent, GFP-MC38 tumor cells were harvested using 5 mM EDTA and washed twice in PBS. MC38 cells in culture medium were mixed with Geltrex and injected subcutaneously into the mouse flanks. Agonistic anti-CD40 treatment or an isotype control antibody was administered intravenously according to treatment protocol. Mice were euthanized, and tumors were collected at defined timepoints after antibody administration. Tumors were then fixed in formalin (10%) and stored at room temperature.

extract_protocol:
Macrophage isolation from digested tumors: Anti-rat IgG Dynabeads were washed and incubated with rat anti-mouse F4/80 IgG2a antibodies and CD11b IgG2b antibodies. Single-cell suspensions from tumors were incubated with anti-CD45 coated Dynabeads on a shaker at 4°C for 30 min. After incubation, a positive selection of Dynabead-bound single-cell suspensions was performed on a DynaMag magnet with three washing steps, as suggested by the manufacturer's instructions.
Single-cell suspensions were fixed following the demonstrated protocol Fixation of cells & Nuclei for Chromium Fixed RNA Profiling (10X Genomics, CG000478) and processed for long-term storage at -80°C. After storage, up to 2 Mio cells per sample were hybridized with unique single Mouse WTA probes using BC001-004 according to the demonstrated protocol Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10X Genomics, CG000527).

value: Keap1 wild-type


title: BMDM Keap1 KO

description: Library name: Keap1KO

value: BMDM

value: Keap1 knockout

value: GM-CSF for 5 days


title: sh2-IP

value: METTL1 knockdown


title: THP-1, ADU-S100, 1 μM

description:
Library name: Sample12
Column name in raw_counts_All_Samples.csv: S0416-A13

value: ADU-S100, 1 μM

value: 4 h


title: Heart, control, replicate1

value: Heart

value: WT

value: Control


title: THP-1, UDSP-Hep, 1 μM

description:
Library name: Sample6
Column name in raw_counts_All_Samples.csv: S0401-A6

value: UDSP-Hep, 1 μM


title: THP-1, ADU-S100, 0.1 μM

description:
Library name: Sample11
Column name in raw_counts_All_Samples.csv: S0416-A12


title: sh2-Input


title: Muscle, miR522, replicate5

value: Muscle

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk36d sgRNA


title: THP-1, UDSP-Hep, 0.1 μM

description:
Library name: Sample5
Column name in raw_counts_All_Samples.csv: S0401-A5

value: UDSP-Hep, 0.1 μM


title: S-CAFs-w13


title: colon carcinoma MC38 tumor from Keap1 knockout mouse 2

description: Library name: KeapKO_tumor_2

value: tumor

value: MC38 (tumor cells)


title: THP-1, ADP-Hep, 10 μM

description:
Library name: Sample4
Column name in raw_counts_All_Samples.csv: S0401-A4

value: Monocyte

value: ADP-Hep, 10 μM


title: Kindey, miR522, replicate5

value: Kindey

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk34d sgRNA


title: Brain, miR522, replicate5

value: Brain

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk35d sgRNA


title: colon carcinoma MC38 tumor from Keap1 knockout mouse 1

description: Library name: KeapKO_tumor_1

value: Keap1 knockout


title: DLD1-W13CM


title: brain_3d_NYKD_rep5

city: Changsha

first: Zhe

last: Yu

address: Kaifu District, Xiangya Road, No.87

institute: Central South University

description: mRNA expression after 3d in the brain of NYKD mice

data_processing:
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.
Assembly: mm10
Supplementary files format and content: The differential expressed genes (DEGs) were screened by the edgeR package (3.22.5) that integrated P < 0.05 and fold change (FC) > 2 or FC < 0.5.

source_name: brain

growth_protocol: Mice were housed in a well-ventilated room (four rats in one cage) at a constant room temperature (25 ± 1℃) and controlled humidity (50 ± 10%), with a 12 h light/dark cycle. All procedures involving the use and care of animals were performed in accordance with the guidelines of Central South University for the care and use of animals and were approved by the Medical Ethics Committee of Central South University (Animal ethical number: XY-20240312003).

extract_protocol:
The total RNA is extracted by standard Trizol RNA extraction. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mice were randomly assigned to three groups: sham, ICH, and NYKD. In the NYKD group, NYKD powder was dissolved in distilled water and administered to mice (5.79 g/kg) by oral gavage once per day for 3 days. The sham and ICH groups were gavaged with an equal dose of distilled water. The mice were sacrificed under 0.3% pentobarbital sodium (60 mg/kg, intraperitoneally) on the 3th day, and transcardially perfused with saline. Brains were harvested and the ipsilateral basal ganglia were isolated immediately.

value: brain

value: gavaged 5.79 g/kg NYKD daily


title: THP-1, ADP-Hep, 1 μM

description:
Library name: Sample3
Column name in raw_counts_All_Samples.csv: S0401-A3

value: ADP-Hep, 1 μM

value: 4 h


title: Lung, miR522, replicate5

value: Lung

value: WT

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk33d sgRNA


title: CRISPR knockout (CRISPR KO) screens on the PC cell line_GEX

city: Shanghai

first: Ke

last: Tang

address: Tongji University, No. 1239, Siping Road, Shanghai

institute: Tongji University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Randger software v2.1.1(https://www.10xgenomics.com/cn/support/software/cell-ranger/latest)
Assembly: hg38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: cell line

extract_protocol:
Pooled sgRNA growth screens in PC9 cells were used to quantify growth phenotypes of sgRNA pairs targeting expressed genes. CRISPR KO PC9 cells expressing dCas9 were transduced with lentiviral particles encoding the dual-sgRNA library by spinfection (1000g) with polybrene (8 ug/ml) to obtain an infection rate of ~40%. Screens were performed in biological replicate with the aim of maintaining 1000 cells per library element for the duration of the screen. Between day 2 and day 6 post-transduction, cells were selected for lentiviral infection using 1 ug/mL puromycin, replenished every 24 hours. On day 7 post-transduction, an aliquot of cells was harvested as an initial time point) The rest of the cell population was passaged for 10 more days and collected at final time point.
For the PC9 day 8 genome-scale experiment, we targeted four metabolic regulator genes and construct non-targeting control sgRNAs accounting for 5% of the total library. Library was performed according to the manufacter's instructions (single cell 3' v2 protocal, 10x Genomics).  To minimize library size while maximizing knockdown, multiplexed CRISPR KO libraries were constructed which targeted each gene with four unique sgRNAs expressed from tandem U6 expression cassettes in a single lentiviral vector, as previously described in Replogle et al. (2020). The Horlbeck et al. (2016) CRISPRi sgRNA libraries were used as a source of sgRNAs targeting each gene, with the optimal sgRNA pair targeting each gene selected based on a balance of empirical data with computational predictions. For genes that produced a significant phenotype in previous CRISPRi screens, sgRNAs were ranked by a discriminant score multiplying the negative log10 p-value by the effect size. Finally, for genes without any empirical evidence, were ranked according to the Horlbeck et al. (2016) hCRISPRi v2.1 algorithm.

value: cell line

tag: library type

value: GEX


title: CRISPR knockout (CRISPR KO) screens on the PC cell line

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Randger software v2.1.1(https://www.10xgenomics.com/cn/support/software/cell-ranger/latest)
Assembly: hg38
Supplementary files format and content: Tab-seperated values files and matrix files
Library strategy: CRISPR screen

value: crispr screen


title: THP-1, PBS

description:
Library name: Sample1
Column name in raw_counts_All_Samples.csv: S0401-A1

value: Monocyte

value: PBS


title: Liver, miR522, replicate5

value: Liver

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk31d sgRNA


title: brain_3d_NYKD_rep3


title: Spleen, miR522, replicate5

value: Spleen

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk32d sgRNA


title: Heart, miR522, replicate5

value: Heart

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk30d sgRNA


title: Human cardiac fibroblasts-Vehicle

city: Little Rock

first: Se-Ran

last: Jun

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

description: Library name: HCF, Veh

data_processing:
The raw sequence data were assessed for quality using fastQC (v0.12.1) and low quality reads and artifical sequences were removed using fastp (v0.23.4).
The raw ATAC-seq data were aligned to the reference genome, GRCh38 'no-alt' assembly from NCBI using bowtie (v2.4.2) with options to produce alignments only for pairs where both reads align properly as a pair.
For post-alignment quality control, mitocondrial reads, duplicates, and ENCODE blacklist regions were removed.
MACS2 (v2.2.9.1) with default significance cut-offs was used to perfrom peak calling and identify genome-wide regions of accessible chromatin with an option of the narrow peak.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: Healthy Male HCFs

growth_protocol: Fibroblast basal medium, 10% fetal bovine serum, insulin (5µg/mL), hFGF-B (1ng/mL), and Gentamicin-Amphotericin (GA-1000; G=30µg/mL, A=15ng/mL), in a humidified incubator at 37°C with 5% CO2. Media was obtained from Lonza.

extract_protocol:
Cells were washed with PBS and gently removed from tissue culture dishes using silicone soft cell lifter, spun down and frozen for nuclei extraction, lirary prep and sequencing by Novogene.
Nuclei were isolated from cell samples, and the nuclei pellet was used as input for transposition using the Vazyme Hyperactive ATAC-Seq Library Prep Kit for Illumina. Transposition reactions were incubated at 37C°C for 30 minutes. Following transposition, equimolar Adapter 1 and Adapter 2 were added, and libraries were amplified by PCR. Final libraries were purified using AMPure XP beads. Initial quantification of libraries was performed using a Qubit 2.0 fluorometer. Libraries were diluted to 1 ng/μL and evaluated for insert size distribution using the NGS3K fragment analyzer. If libraries met expected size profiles, the accurate molar concentration was determined via qPCR. Libraries with effective concentrations >2 nM were pooled in equimolar amounts for sequencing.

treatment_protocol: Cells with treated with 200 μM oleate:palmitate mix (bound to BSA)- FA mix for 48 hours, or vehicle (BSA)

value: Heart (ventricle)

value: Cardiac ventricular fibroblasts

value: Male

value: Vehicle (Veh)


title: brain_3d_NYKD_rep1

value: brain

value: WT

value: gavaged 5.79 g/kg NYKD daily


title: Human cardiac fibroblasts-Fatty Acid

description: Library name: HCF, FA

value: fatty acid (FA)


title: Muscle, miR422, replicate4

value: Muscle

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk29d sgRNA


title: small1

city: Hefei

first: Mingming

last: Zhu

state: Anhui

address: No.96, JinZhai Road Baohe District,

department: life sciences and medicine

institute: University of Science and Technology of China

description:
small_barcodes.tsv.gz
small_matrix.mtx.gz
small_features.tsv.gz

data_processing:
The Raw data (FASTQ files) for each sample were matched to the hg19 reference genome. The quantification of UMI counts was performed using the 10×Genomics Cell Ranger pipeline (V3.1.0) with default setting
Quality control and dimensionality reduction analyses were conducted using R version 4.1.2 and the Seurat package version.We created Seurat objects for small and large AML cells were filtered using the following criteria: unique RNA features between 500 and 4000 and less than 10% of mitochondrial genes. Moreover, genes with expression observed in less than 5 cells were excluded from the analysis. Then, we used the "IntegrateData" function to integrate the two datasets together.
Assembly: hg19
Supplementary files format and content: UMI count for each cell in mtx format and cell barcodes/genes in tsv format

source_name: small cells of bmmncs lin-

extract_protocol:
Human AML Lin- immature cells were purified from primary human AML bone marrow using magnetic activated cell sorting kit with lineage negative magnetic beads (Miltenyi Biotec, 130-092-211) following manufacturer’s instructions.  The purity reached more than 95%.For the scRNA-seq analysis of human AML lin- small and large cells,  small cells and large cells derived from bone marrow lin- cells of 4 AML patients were sorted using the CytoFLEX cell analyzer (Beckman Coulter Life Sciences, Indianapolis, United States) );.we pooled 4 sample from the small group in one tube and 4 sample from the large group in another tube..We then counted and resuspended the pooled cells at a concentration of 1000 cells/µL, targeting an estimated 6000 cells per library, following the instructions of the Single Cell 3ʹ Solution v3 Kit (10X Genomics).
Single-cell libraries were constructed strictly according to the manufacturer's standard protocol. Each sequencing library is generated using a unique sample index. Libraries were sequenced on the Illumina NovaSeq 6000 System.

value: small cells of bmmncs lin-

tag: disease

value: acute myeloid leukemia


title: Brain, miR422, replicate4

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a NNNNNNNNNNNNNN(private) \ -g NNNNNNNNNNNNNNNNNNNNN(Private) \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table

value: Brain

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk28d sgRNA


title: RD_shDHCR7_samp_4

city: Helsinki

first: Nebeyu

middle: Yosef

last: Gizaw

state: Helsinki

address: Haartmaninkatu

department: Biomedicine

country: Finland

institute: University of Helsinki

data_processing:
The analysis from the generated FASTQ data was performed using Chipster software (www.chipster.csc.fi) (Kallio et al., 2011).   .
The quality of FASTQ files were assessed with FASTQC, and used as input for alignment to reference genome using HISAT2 (Kim et al., 2015).
Aligned reads per gene were counted with HTseq (Anders et al., 2015) and DEseq2 (Love et al., 2014) was used to anayze differentially expressed genes.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were used and statistical significance of adjusted P-value (FDR) < 0.05 was set as cut off, and the final values were log2 transformed
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: raw counts of sequencing reads

source_name: RD cell line

growth_protocol: RD cells were cultured in Dulbecco's Modified Eagle Medium (DMEM high glucose) supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, penicillin (100U/ml) and streptomycin (100U/ml) and maintained at 37ºC in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA from the lysed cells was extracted with Nucleospin RNA II Kit (Macherey-Nagel).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to generate cDNA libraries for next generation sequencing.

value: RD cell line

value: DHCR7 knockdown


title: large2

description:
large_barcodes.tsv.gz
large_matrix.mtx.gz
large_features.tsv.gz

source_name: large cells of bmmncs lin-

value: large cells of bmmncs lin-


title: brain_3d_ICH_rep5

value: gavaged distilled water daily


title: brain_3d_ICH_rep1


title: RD_shDHCR7_samp_3


title: brain_3d_NYKD_rep4


title: THP-1, ADP-Hep, 0.1 μM

first: Yuanhanyu

address: No.7, Science Park Road, Zhongguancun Life Science Park, Beijing

institute: National Institute of Biological Sciences

description:
Library name: Sample2
Column name in raw_counts_All_Samples.csv: S0401-A2

value: Monocyte

value: ADP-Hep, 0.1 μM

value: 4 h


title: large1


title: SUDHL2, IgG, CUT&RUN, CC99282

city: San Diego

first: Antonia

last: Lopez-Girona

state: California

address: 10300 Campus Point Drive

department: Protein Homeostasis TRC

institute: Bristol Myers Squibb

data_processing:
Paired-end sequencing reads were mapped to human genome (hg38) using bowtie2 (version 2.2.5), with the parameters “--end-to-end --no-unal --no-mixed --no-discordant --phred33”. Only concordantly aligned reads were kept. Subsequently, the resulting files in BAM format were sorted and indexed. Duplicate reads were marked using the markdup command from sambamba (version 0.6.6) and then removed. Bigwig files were generated by the bamCoverage command from deeptools (version 3.5.1), with 20bp as resolution and count per million reads as the normalization method (bamCoverage --binSize 20 --extendReads --smoothLength 60 --normalizeUsing CPM --blackListFileName $blacklistFile). Signals contributed by reads mapped to blacklisted regions were removed.
MACS2 (version 2.2.7.1) was used to identify peaks with narrowPeak mode and q-value 0.05 as the statistic cutoff. To identify IKAROS and AIOLOS’ co-binding peaks, we first unified peak coordinates between IKAROS and AIOLOS. Specifically, a peak set with unified coordinates was generated by the merge command from bedtools. Then the unified peaks showing overlap with IKAROS (or AIOLOS) peaks were deemed as the new IKAROS (AIOLOS) peaks and used for further analyses. The IKAROS and AIOLOS peaks with the unified coordinates were compared by the intersect command from bedtools suite (version 2.30.0), where the common peaks were identified as peaks co-bound by IKAROS and AIOLOS.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&RUN

growth_protocol: RPMI + 10% FBS + 1X NEAA + 1% L-Glutamin. Cells were cultured at 37C at 5% CO2

extract_protocol:
0.01% digitonin was used to premeabilize the cells and Mnase was used to cleave antibody-bound chromatin
NEBNext® UltraTM II DNA Library Prep Kit for Illumina from New England BioLabs. A maxiumum of 10ng was used as starting material. Libraries were amplified using 14 cycles on thermocycler. Libraries were purified using AmpureXP beads from Beckman Coulter. Libraries were validated using Agilent high sensitivity DNA kit

treatment_protocol: DMSO or 40nM of CC99282

value: DLBCL

tag: cut&run antibody

value: IgG (Epicypher, SKU 13 0042)


title: brain_3d_ICH_rep4

value: brain

value: WT


title: Kindey, miR422, replicate4

extract_protocol:
Genomic DNA was extracted from tissues using TIANamp Genomic DNA Kit (DP304, Tiangen, China)
The sgRNA-targeted loci were amplified using Taq PCR MasterMix (KT211, Tiangen, China) and purified by TIANgel Purification Kit (DP219, TIANGEN).
Amplicon-seq

value: Kindey

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk27d sgRNA


title: Liver, control, replicate1

value: Liver

value: Control


title: small2

value: small cells of bmmncs lin-

value: acute myeloid leukemia


title: SUDHL2, Aiolos, CUT&RUN, CC-99282

value: Aiolos (CST,  #15103S)


title: RD_shDHCR7_samp_1

value: RD cell line

value: DHCR7 knockdown


title: brain_3d_NYKD_rep2

value: gavaged 5.79 g/kg NYKD daily


title: brain_3d_ICH_rep3

value: gavaged distilled water daily


title: SUDHL2, Ikaros, CUT&RUN, CC-99282

value: Ikaros (CST,  #14859S)


title: colon carcinoma MC38 tumor from Keap1 wild-type mouse 1

description: Library name: KeapWT_tumor_1

value: tumor

value: MC38 (tumor cells)

value: Keap1 wild-type


title: RD_Control_samp_4

value: control


title: brain_3d_ICH_rep2

value: brain

value: WT


title: Liver, miR422, replicate4

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk24d sgRNA


title: MC38 tumor at 24 hours post–irradiation

description: Library name: 24h

value: MC38 tumor cells

value: irradiation with 12Gy


title: Heart, miR422, replicate4

value: Heart

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk23d sgRNA


title: RD_Control_samp_3


title: RD_Control_samp_2


title: SUDHL2, Aiolos, CUT&RUN, DMSO

value: DLBCL

value: DMSO, 6h

value: Aiolos (CST,  #15103S)


title: SUDHL2, Ikaros, CUT&RUN, DMSO


title: brain_3d_sham_rep3


title: Lung, miR422, replicate4

value: Lung

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk26d sgRNA


title: Brain, miR122, replicate3

source_name: Brain

value: Brain

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk21d sgRNA


title: Muscle, miR122, replicate3

source_name: Muscle

value: Muscle

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk22d sgRNA


title: Kindey, miR122, replicate3

value: Kindey

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk20d sgRNA


title: prefrontal cortex ,MS_EC12 group  ,rep 6

city: Tokyo

first: Eman

middle: Abdo

last: Mady

address: Harumicho

department: veterinary medicine

country: Japan

institute: Tokyo university Of Agriculture and technology

description: Library name: MS_EC6

data_processing:
Data integrity and quality control of the sequenced raw reads were checked by FastQC v0.11.7 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Overall reads’ quality, total bases, total reads, GC (%), and basic statistics were calculated. To reduce biases in the analysis, artifacts such as low-quality reads, adaptor sequences, contaminant DNA, or PCR duplicates were removed using Trimmomatic 0.38 software (http://www.usadellab.org/cms/?page=trimmomatic).
Trimmed readings are mapped to the reference genome with HISAT2 version 2.1.0 (https://ccb.jhu.edu/software/hisat2/index.shtml), a splice-aware aligner. To map cDNA fragments obtained from RNA sequencing, mm10 was used as a reference genome. After the read mapping, the transcript was assembled by StringTie version 2.1.3b (https://ccb.jhu.edu/software/stringtie/)  with aligned reads. Transcripts were additionally assembled from the results of mapped reads to predict novel transcripts and novel alternative splicing transcripts without the StringTie-e option. The assembled annotation (GTF file) of samples was merged into one merged file with the StringTie-merge option. Then, the abundances of samples were calculated for known and novel transcripts.
Expression profiles were represented as read count and normalization values which were calculated based on transcript length and depth of coverage. Normalization values were provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million)
In groups with different conditions, genes or transcripts that expressed differentially were filtered out through statistical hypothesis testing. Differentially Expressed Genes (DEG) analysis was performed on 4 comparison pairs as requested using DESeq2
Assembly: (Reads Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted from the prefrontal cortex using the ISOGEN II Reagent (Nippon Gene Co., Ltd, Tokyo, Japan). The quality of the isolated total RNA was confirmed and the grade of RNA in all samples was unified.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Mice were euthanized for brain sample collection and molecular assessments and then these samples Kept in dry ice during the collection and then these samples stored at - 80°C until further analysis

value: brain

value: prefrontal cortex

value: wild type

value: MS , EC-12 treatment


title: RD_Control_samp_1

value: RD cell line

value: control


title: RD_shDHCR7_samp_2

value: DHCR7 knockdown


title: brain_3d_sham_rep1

value: WT

value: gavaged distilled water daily


title: Lung, miR122, replicate3

source_name: Lung

value: Lung

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk19d sgRNA


title: ATAC OE-YTHDF3-4-Rep1

city: Guangzhou

first: Li

last: Xinhui

address: Guangzhou

institute: Sun Yat-sen university

data_processing:
The Paired-end raw reads were mapped to the human reference genome (hg19) with Bowtie2 after adapter sequences were trimmed.
The reads were then filtered for mitochondrial reads, low-quality reads, PCR duplicates, and black list regions. The peak calling of each sample was performed by MACS2.
Peak counts were combined into an N × M matrix and then be normalized by R package DiffBind, where N represents called peaks, M represents the samples, and each value Di,j represents the peak intensity for respective peak i in sample j.
The HOMER's promoter analysis was used to identify enriched motifs for differential peak set. The differential analysis was conducted using Wilcoxon's-test.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: breast

growth_protocol: All MDA-MB-231 cell lines were grown in DMEM medium (HyClone) with 10% FBS (ExCell Bio) and 1% penicillin-streptomycin (Gibco).

extract_protocol:
ATAC–seq of HOTAIR-Ctrl, HOTAIR-OE, HOTAIR-Ctrl YTHDF3-KO and HOTAIR-OE YTHDF3-KO cells were performed as previously described (Corces et al., 2017). Briefly, 50000 cells were pelleted, resuspended in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40, and immediately centrifuged at 500g for 10 min at 4 °C. The nuclei pellets were resuspended in 50 μl of transposition buffer (25 μl of 2× TD buffer, 22.5 μl of distilled water, 2.5 μl of Illumina Tn5 transposase) and incubated at 37 °C for 30 min. Transposed DNA was purified with the DNA Clean & Concentrator-5 kit (Zymo Research), and eluted in 10 μl of EB buffer.
Library fragments were amplified using NEBnext PCR master mix as previously described (Corces et al., 2017)

value: breast

value: MDA-MB-231 cell

value: breast cancer cell

value: HOTAIR-OE YTHDF3-KO


title: brain_3d_sham_rep2


title: ATAC OE-YTHDF3-2-Rep2


title: Spleen, miR422, replicate4

city: Beijing

value: Spleen

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk25d sgRNA


title: SUDHL2, IgG, CUT&RUN, DMSO

value: DLBCL

value: DMSO, 6h

value: IgG (Epicypher, SKU 13 0042)


title: CNTNAP2-203-3

city: Hengyang City

first: Suzhen

last: Ma

state: Hunan Province

address: 28 Changsheng West Road, Hengyang City, Hunan Province

institute: University of South China

data_processing:
Adapter and low-quality reads were first trimmed using Trim Galore (version 0.4.4) in paired-end mode with default parameters. Trimmed reads were then mapped to the hg38 reference genome to count mapped reads for all human transcripts.
Assembly: hg38
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 log2(FPKM) values for each Sample

growth_protocol: CAL27 cells were cultured in Dulbecco’s modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum (FBS, Sigma, USA).

extract_protocol:
Extraction of total RNA following the manufacturer’s instruction of the AllPrep DNA/ RNA/miRNA Universal Kit (80224, Qiagen, USA).
For library preparation, 1 mg of total RNA from each sample was depleted for rRNA using the Ribo−Zero rRNA Removal Kit (RZH1046, EPICENTRE, USA), followed by construction of sequencing library using the TruSeq RNA Sample Prep Kit v2 (RS−122, Illumina, USA).

treatment_protocol: Constructing stable cell lines of CAL27 with overexpression of CNTNAP2-203:Lentiviral particles containing the control vector or CNTNAP2-203, were individually produced in HEK_x001E_293T cells. The supernatants containing the lentiviral particles were harvested. OSCC cells were infected with the respective lentiviruses, followed by selection with 5 μg/ml puromycin (Beyotime, China) for 2 weeks.

value: oral squamous cell carcinoma

value: CNTNAP2-203 OE


title: prefrontal cortex ,MS_EC12 group  ,rep 4

description: Library name: MS_EC4

value: brain

value: prefrontal cortex

value: wild type

value: MS , EC-12 treatment


title: Spleen, miR122, replicate3

value: WT

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk18d sgRNA


title: ATAC OE-YTHDF3-2-Rep1

value: breast


title: brain_3d_sham_rep5

value: gavaged distilled water daily


title: brain_3d_sham_rep4


title: prefrontal cortex ,MS_EC12 group  ,rep 3

description: Library name: MS_EC3


title: Liver, miR122, replicate3

source_name: Liver

value: Liver

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk17d sgRNA


title: CNTNAP2-203-2


title: prefrontal cortex ,MS_EC12 group  ,rep 2

description: Library name: MS_EC2


title: ATAC OE-YTHDF3-1-Rep2

value: MDA-MB-231 cell

value: breast cancer cell

value: HOTAIR-OE YTHDF3-KO


title: ATAC OE-YTHDF3-4-Rep2


title: ATAC OE-YTHDF3-1-Rep1


title: CNTNAP2-203-1


title: prefrontal cortex ,MS_EC12 group  ,rep 5

description: Library name: MS_EC5


title: prefrontal cortex ,MS_EC12 group  ,rep 1

description: Library name: MS_EC1


title: Muscle, miR122, replicate2

value: Muscle

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk15d sgRNA


title: prefrontal cortex , Control_EC12group ,rep 6

description: Library name: C_EC6

value: EC-12 treatment


title: ATAC OE-YTHDF3-5-Rep2

value: HOTAIR-OE


title: Control2

value: oral squamous cell carcinoma


title: ATAC OE-YTHDF3-5-Rep1


title: prefrontal cortex , Control_EC12group,rep 5

description: Library name: C_EC5

value: brain

value: prefrontal cortex


title: Brain, miR122, replicate2

value: Brain

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk14d sgRNA


title: Control1

description:
CAL27_EGFP_1
The 'R2' (reverse read) library file was missing; 'R1' file was submitted as single-end.

value: WT


title: ATAC OE-puro-3-Rep2

value: breast


title: Lung, miR122, replicate2

value: Lung

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk12d sgRNA


title: prefrontal cortex , Control_EC12group ,rep 4

description: Library name: C_EC4

value: wild type


title: RBP4-KO

city: Taian

first: Yingli

last: Shang

state: Shandong

address: No. 61, Daizong Street

institute: Shandong Agricultural University

description: Library name: Sample2

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Hisat2 (v2.0.1) was used to index reference genome sequence, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: bone marrow

growth_protocol: Murine BMDMs were obtained and maintained in DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor.

extract_protocol:
RNA was harvested using the total RNA purification kit (Promega). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

value: bone marrow

value: BMDMs

value: Bone marrow derived macrophages


title: WT

description: Library name: Sample1


title: ATAC OE-P18-Rep2

value: MDA-MB-231 cell

value: breast cancer cell


title: Kindey, miR122, replicate2

source_name: Kindey

value: Kindey

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk13d sgRNA


title: ATAC OE-puro-3-Rep1

value: HOTAIR-OE


title: prefrontal cortex , Control_EC12group ,rep 3

description: Library name: C_EC3

value: brain

value: EC-12 treatment


title: Heart, miR122, replicate3

source_name: Heart

value: Heart

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk16d sgRNA


title: prefrontal cortex , Control_EC12group  ,rep 2

description: Library name: C_EC2

value: prefrontal cortex


title: Spleen, miR122, replicate2

source_name: Spleen

value: Spleen

value: WT

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk11d sgRNA


title: prefrontal cortex , Control_EC12 group ,rep 1

description: Library name: C_EC1

value: wild type


title: ATAC OE-P18-Rep1

value: breast


title: Liver, miR122, replicate2

value: Liver

value: AAV-TNT4-TadA8e-SpRY N aa2-713-InteinN-miR122 TS + AAV-CASI-InteinC-SpRY C aa714-1368-U6-Camk10d sgRNA