title: MSK_4975__R2


title: MSK_4943__R1

status: Public on Nov 01 2025

type: SRA

city: New York

first: Madelyn

last: Espinosa-Cotton

state: New York

address: 1275 York Ave

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Gene counts were generated by alignment to human transcriptome GRCh38 using STAR in RSEM.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: txt file with count data from RSEM

molecule: total RNA

organism: Homo sapiens

source_name: DSRCT

extract_protocol:
Phase separation in OCT frozen tissue lysed in TRIzol was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher catalog # A27828) on the KingFisher Flex Magnetic Particle Processor (Thermo Scientific catalog # 5400630) according to the manufacturer’s protocol
179-700 ng of total RNA with DV200 percentages varying from 3-78% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

tag: tissue

value: DSRCT

tag: patient

tag: Sex

value: Male

tag: fusion protein_identified

value: Yes

tag: survival (years)


title: Inguinal LN_cd169_1

city: Philadelphia

first: Aliia

middle: R

last: Fatkhullina

state: Pennsylvania

address: 3400 Civic Center Blvd Bldg 421

institute: University of Pennsylvania

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm) were scaled by gene length
Initial filtering removed genes with higher than 2 counts per million (cpm) expression in isotype control (to filter out potential non-specific, non-CD169 genes), then genes that have a cpm > 2 were used for the analysis.
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value < 0.05 were considered significant for downstream analysis
Assembly: mm10
Supplementary files format and content: comma separated variable files with raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: lymph node

extract_protocol:
RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.
500-1000ng of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

treatment_protocol: RiboTag mice were crossed to a CD169-Cre recombinase-expressing mouse to activate the Rpl22HA allele in all tissues. Homozygous CD169RPL22HA mice lymph nodes were collected and used for the RiboTag immunoprecipitation.

value: lymph node

tag: genotype

value: CD169 Cre KI/KI, Rpl22HA homozygous

tag: cell type

value: cd169 macrophages


title: KO-CNV-4

city: Shanghai

first: Yue

last: Zou

address: Shanghai

country: China

institute: Eye & ENT Hospital, Fudan University

description: Library name: 4

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: retina

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: retina

value: PD-L1 knockout


title: WT-CNV-2

description: Library name: 6

value: control


title: ST_52T__Lt

city: Ramat Gan

first: Maya

last: Dadiani

state: Please Select

address: Tel Hashomer

country: Israel

institute: Sheba Medical Center

data_processing:
Illumina adapters and PolyA/T stretches were trimmed using cutadapt
reads were mapped to the human genome (GRCh38) using STAR v2.4.2a
Counting proceeded over genes annotated in Ensembl release 88, using HTSeq-count
Normalization with DESeq2 (1.10.1)
Assembly: GRCh38
Supplementary files format and content: DESeq2 Normalized counts

source_name: breast cancer tumor

extract_protocol:
FFPE tumor samples were macro-dissected to enrich for tumor cellularity. The 5 microns sections were deparaffinized at 90°C for 5 min. Total RNA was extracted using nucleic acid isolation kit (AllPrep® Qiagen) according to protocol instructions.
mRNA-seq libraries were constructed by Truseq RNA Sample preparation kit v2 (illumina).

treatment_protocol: Chemotherapy treatment included a standard-of-care sequential doxorubicin and cyclophosphamide followed by paclitaxel, and additional Herceptin for HER2+ patients

value: breast cancer tumor

tag: treatment

value: post-treatment

tag: breast cancer_pathological_subtype

value: ER+


title: Celiac LN_cd169_1


title: MSK_4975__R1


title: ST_52N__Lt

source_name: Normal breast tumor adjacent

value: Normal breast tumor adjacent


title: ST_52C__Rt

value: pre-treatment


title: Ceco-colonic LN_cd169_1


title: ST_52T__Rt


title: MSK_5038A_R1


title: WT-CNV-1

description: Library name: 5


title: KO-CNV-2

description: Library name: 2


title: Deep Cervical LN_cd169_1


title: KO-CNV-1

description: Library name: 1


title: Inguinal LN MSM_3

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input and normalized using limma/voom (edgeR)
Assembly: mm10
Supplementary files format and content: comma separated variable file for raw counts for each sample
Supplementary files format and content: .tsv files containing kallisto alignment output (estimated counts, TPM, and effective length) for each sample
Supplementary files format and content: comma separated variable file for normalized counts per million (CPM) for each sample

extract_protocol:
Macrophages were sorted into TCL buffer containing 1% 2-mercaptoethanol. RNA was isolated using RNA Clean XP beads (Agentcourt) on a magnetic stand.
cDNA libraries were constructed using Nextera XT Index Kit according to the manufacturer’s protocol.

treatment_protocol: To address the role of lymph node (LN) macrophages in the regional specificity of gut-draining lymph nodes, we sorted subcapsular sinus macrophages (SCM, CD169+F4/80-), medullary sinus macrophages (MSM, CD169+F4/80+), medullary cord macrophages (MCM, CD169-F4/80+) from duodenum (Duo), jejunum (Jej), ileum (Ile), ceco-colonic (Col), and inguinal (Ing, as non-gut reference) LNs and performed bulk RNAseq analysis.

value: medullary sinus macrophages (MSM)

tag: age


title: ST_49T


title: MSK_4931__R2


title: ST_56C_B


title: KO-CNV-3

description: Library name: 3


title: Ileal LN_cd169_1


title: MSK_4927__R1

value: No


title: Inguinal LN MSM_1


title: MSK_4931__R1


title: ST_49C


title: ST_52C__Lt


title: Vitamin A deficient Inguinal LN 5

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value (adj_pval) < 0.05 were considered significant for downstream analysis
Assembly: mm10
Supplementary files format and content: comma separated variable files for raw counts for each sample

extract_protocol:
RNA was extracted using TRIZOL protocol, RNA samples were purified using RNAclean XP beads (Beckman Coulter), and RNA concentration was measured with a NanoDrop Microvolume Spectrophotometer (Thermo Fisher).
1000-1500 µg of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

treatment_protocol: To study the role of Vitamin A on gut-draining lymph nodes regionalization, 7-8 weeks old C57BL/6J females were placed on a vitamin A deficient (TD.86143, Inotiv) or ingredient matched control with vitamin A added back at 20 IU/g (TD.91280, Inotiv) 3 weeks before breeding set up. Second adn third litters were sacrificed at 8 (postnatal day 56) weeks old.

value: female

value: postnatal day 56

tag: diet

value: Vitamin A deficient diet


title: Inguinal LN MSM_2


title: Jejunal LN_cd169_1


title: ST_48N


title: MSK_4927__R2

value: DSRCT

value: Male


title: MSK_4921__R2


title: MSK_4919__R2


title: ST_49N


title: MSK_4921__R1


title: Ceco-colonic LN MSM_3

value: lymph node


title: Vitamin A deficient Jejunal LN 5


title: MSK_4919__R1


title: Vitamin A deficient Ileal LN 5


title: Ceco-colonic LN MSM_2


title: ST_47T


title: Ceco-colonic LN MSM_1


title: Duodenal LN_cd169_1

value: CD169 Cre KI/KI, Rpl22HA homozygous

value: cd169 macrophages


title: ST_47N


title: MSK_4918__R2

value: Yes


title: Ileal LN MSM_3


title: Vitamin A deficient Inguinal LN 4


title: ST_47C


title: Vitamin A deficient Colonic LN 5


title: Vitamin A deficient Duodenal LN 5


title: MSK_4918__R1


title: ST_43T


title: Ileal LN MSM_1


title: MSK_4916__R2


title: MSK_4916__R1


title: ST_43C


title: Vitamin A deficient Colonic LN 4


title: Jejunal LN MSM_3


title: Ileal LN MSM_2


title: MSK_4915C_R2


title: ST_42N

value: TNBC


title: ST_42T

value: breast cancer tumor


title: Jejunal LN MSM_2


title: Vitamin A deficient Duodenal LN 4


title: MSK_4915C_R1


title: Jejunal LN MSM_1


title: Vitamin A deficient Inguinal LN 3


title: MSK_4915A_R2


title: ST_42C


title: Vitamin A deficient Colonic LN 3


title: Duodenal LN MSM_3


title: MSK_4915A_R1


title: ST_35T

value: post-treatment


title: ST_43N

value: ER+


title: Vitamin A deficient Ileal LN 3


title: MSK_4895B_R2


title: ST_35N

value: Normal breast tumor adjacent


title: Vitamin A deficient Ileal LN 4


title: Vitamin A deficient Jejunal LN 3


title: MSK_4895B_R1


title: Duodenal LN MSM_1


title: ST_35C

value: pre-treatment


title: ST_32T


title: Inguinal LN MCM_3

value: medallury cord macrophages (MCM)


title: Vitamin A deficient Jejunal LN 4


title: Vitamin A deficient Duodenal LN 3


title: Inguinal LN MCM_2


title: MSK_4895A_R1


title: Vitamin A deficient Inguinal LN 2


title: Ceco-colonic LN MCM_3


title: MSK_4892__R2


title: Vitamin A deficient Ileal LN 2


title: Duodenal LN MSM_2

value: medullary sinus macrophages (MSM)


title: ST_32C


title: ST_31T


title: Ceco-colonic LN MCM_2


title: MSK_4892__R1


title: Vitamin A deficient Jejunal LN 2

value: female


title: Ceco-colonic LN MCM_1


title: MSK_4832__R2


title: Vitamin A deficient Duodenal LN 2

value: postnatal day 56


title: ST_31N


title: MSK_4832__R1


title: MSK_4895A_R2


title: ST_31C


title: Ileal LN MCM_3


title: MSK_4807D_R1

value: Female


title: MSK_4807D_R2

value: DSRCT


title: Vitamin A deficient Inguinal LN 1

value: Vitamin A deficient diet


title: Inguinal LN MCM_1

value: lymph node


title: Vitamin A deficient Ileal LN 1


title: Vitamin A deficient Colonic LN 1


title: ST_29N


title: ST_32N


title: ST_29C


title: Vitamin A deficient Colonic LN 2


title: Ileal LN MCM_1


title: Ileal LN MCM_2


title: MSK_4807C_R2


title: Jejunal LN MCM_3


title: ST_28T


title: Vitamin A deficient Jejunal LN 1


title: Jejunal LN MCM_2


title: MSK_4807B_R2


title: Vitamin A deficient Duodenal LN 1


title: Duodenal LN MCM_3


title: ST_24T


title: MSK_4807B_R1


title: Vitamin A sufficient Colonic LN 5

value: male

value: Vitamin A sufficient (control)


title: MSK_4801__R2

value: Male

value: Yes


title: ST_24C

value: breast cancer tumor


title: ST_23T

value: post-treatment


title: MSK_4801__R1


title: Duodenal LN MCM_1


title: Vitamin A sufficient Jejunal LN 5


title: Inguinal LN SCM_3

value: subcapsular sinus macrophages (SCM)


title: Vitamin A sufficient Duodenal LN 5


title: MSK_4781__R2


title: ST_23N

value: Normal breast tumor adjacent

value: ER+


title: Inguinal LN SCM_2


title: Vitamin A sufficient Inguinal LN 4


title: MSK_4753__R2


title: ST_28N


title: MSK_4781__R1


title: Vitamin A sufficient Colonic LN 4


title: ST_28C

value: pre-treatment


title: Inguinal LN SCM_1


title: Ceco-colonic LN SCM_3


title: Jejunal LN MCM_1

value: medallury cord macrophages (MCM)


title: MSK_4753__R1


title: MSK_4746__R2

value: Not Available


title: ST_14N


title: Vitamin A sufficient Ileal LN 4

value: postnatal day 56


title: Vitamin A sufficient Jejunal LN 4


title: MSK_4746__R1


title: Ileal LN SCM_3


title: ST_13T


title: DU145-EV cells, DEX, 24 hours

city: Rehovot

first: Arunachalam

last: Sekar

address: Herzl street

department: IRB

institute: Weizmann Institute of Science

data_processing: none provided

growth_protocol: VCaP, DU145-EV ans DU145-tERG cells were maintained in RPMI media suplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Rnaeasy mini kit (Qiagen). 50ng of total RNA was used for seqeunce library preperation.
RNA libraries for RNA seq was prepared using MARS-seq inhouse protocol.

treatment_protocol: 24 hours prior treatment cells were grown in 10% charcoal streipped media (CSS). CSS grown cells were treated with either veh or DEX (1uM, Sigma) for 24 hours.

tag: cell line

value: Human prostate cancer cells

value: Empty vector

value: DEX


title: DU145-EV cells, Veh, 24 hours

value: Vehicle


title: ST_13N_B


title: Ileal LN SCM_2

value: lymph node


title: Vitamin A sufficient Colonic LN 3

value: male

value: Vitamin A sufficient (control)


title: ST_14T


title: ST_13C


title: DU145-tEREG cells, DEX, 24 hours

value: tERG overexpression


title: Ileal LN SCM_1


title: Vitamin A sufficient Ileal LN 3


title: ST_12T

value: breast cancer tumor


title: DU145-tERG cells, Veh, 24 hours


title: Ceco-colonic LN SCM_2


title: Jejunal LN SCM_3


title: Vitamin A sufficient Jejunal LN 3


title: ST_16C


title: ST_14C


title: VCaP cells, DEX, 24 hours

source_name: VCaP

value: VCaP


title: Vitamin A sufficient Duodenal LN 3


title: Ceco-colonic LN SCM_1

value: subcapsular sinus macrophages (SCM)


title: Vitamin A sufficient Inguinal LN 3


title: ST_12N

value: Normal breast tumor adjacent

value: post-treatment


title: Vitamin A sufficient Duodenal LN 4


title: Jejunal LN SCM_1


title: ST_12C

value: pre-treatment

value: ER+


title: Vitamin A sufficient Inguinal LN 2

value: female


title: DU145-tERG cells, DEX, 1 hour

library_source: genomic

molecule: genomic DNA

growth_protocol: VCaP and DU145-tERG cells were maintained in RPMI media suplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quencing and cell lysis, chromatin was sonicated using a E220 focused ultra sonicator (Covaris)
ChIP seq libraried were prepared using the KAPA HTP library preparation kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermal cycler. Post amplificationlibraried were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High sensitivity DNA kit.

treatment_protocol: 24 hours prior treatment cells were grown in 10% charcoal streipped media (CSS). CSS grown cells were treated with either veh or DEX (1uM, Sigma) for 1 hour.

tag: chip antibody


title: ST_11N_B


title: Duodenal LN SCM_3


title: Vitamin A sufficient Colonic LN 2

value: postnatal day 56


title: Duodenal LN SCM_2


title: DU145-tERG cells, Veh

value: Human prostate cancer cells


title: ST_11C


title: DU145-tERG cells, DEX, 1 hour, GR


title: DU145-tERG cells, Veh, GR


title: Vitamin A sufficient Inguinal LN 5


title: Duodenal LN SCM_1


title: ST_10T


title: Vitamin A sufficient Jejunal LN 2


title: Jejunal LN SCM_2


title: Rag1-/- inguinal LN_4

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value (adj_pval) < 0.05 were considered significant for downstream analysis
Assembly: mm10
Supplementary files format and content: comma separated variable files for raw counts for each sample
Supplementary files format and content: .tsv files containing kallisto alignment output (estimated counts, TPM, and effective length) for each sample

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit (Thermo Fisher) according to the manufacturer’s instructions.
1000-1500 ng of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

treatment_protocol: To examine the transcriptional differences between gut-draining lymph nodes (duodenum (Duo), jejunum (Jej), ileum (Ile), ceco-colonic (Col), and inguinal (Ing, skin-draining, as non-gut reference)) with a lack of adaptive immune cells (mature T and B cells), we performed bulk RNAseq on whole LNs from Rag1-/- (B6.129S7-Rag1tm1Mom/J) mice.


title: VCaP cells, Veh, 24 hours


title: Vitamin A sufficient Duodenal LN 2


title: ST_10N_B


title: DU145-tERG cells, Veh, ERG


title: DU145-tERG cells, DEX, 1 hour, ERG


title: ST_11T


title: Rag1-/- ceco-colonic LN_4


title: Vitamin A sufficient Inguinal LN 1


title: ST_10C


title: Rag1-/- ileum LN_4


title: Vitamin A sufficient Colonic LN 1


title: VCaP cells, DEX, 1 hour


title: Rag1-/- jejunum LN_4


title: VCaP cells, Veh


title: ST_8T


title: Rag1-/- duodenum LN_4


title: Vitamin A sufficient Ileal LN 1


title: ST_8N_C


title: VCaP cells, Veh, GR


title: ST_8C


title: VCaP cells, DEX, 1 hour, GR


title: ST_7T


title: Vitamin A sufficient Ileal LN 5


title: Rag1-/- inguinal LN_3


title: ST_23C


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(+), Ribo-seq, replicate 2

city: Sendai

first: Masaki

last: Hosogane

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku university

description:
Library name: Sample16
V4_48_pls_2

library_source: other

data_processing:
Sequence data were processed as previously described but with modifications (Methods 126, 112-129, 2017.). In brief, adapter trimming was performed with fastp v.0.21.0, and reads were mapped to noncoding RNA (ncRNA) sequences with the use of STAR v.2.7.0a to remove reads that originated from rRNA genes and other ncRNA genes in silico. The remaining reads were aligned to the human genome hg38 and assigned to the GENCODE Human release 32 reference from the UCSC Genome Browser (https://genome.ucsc.edu/index.html) with the use of STAR 2.7.0a.
Mapped reads were counted for each Ensembl transcript ID using the GENCODE human reference (release 32)
Assembly: The human genome hg38 and the GENCODE Human release 32 reference
Supplementary files format and content: counts.gene.csv contains raw (unnormalized) read counts at the Ensembl transcript level (one transcript per row). Columns are: (1) Ensembl transcript ID (ENST), (2) transcript length (nt), (3–10) Ribo-seq sample counts, (11–18) RNA-seq sample counts, (19) gene symbol, and (20) gene description.
Supplementary files format and content: The first row contains column headers: V0_3 cells carry the dox-inducible KTN1 V2(−) construct, while V4_48 cells carry the dox-inducible KTN1 V2(−) construct. min indicates DOX(-), while pls indicates DOX(+)
Library strategy: Ribo-Seq

molecule: other

source_name: HeLa

growth_protocol: Cells were maintained under 5% CO2 at 37C in DMEM supplemented with 1 mM sodium pyruvate, 1% MEM nonessential amino acids, penicillin (100 U/ml), streptomycin (100 μg/ml), 2 mM L-glutamine, and 10% FBS.

extract_protocol:
For Ribo-seq, ~3 million cells were lysed in 400 μl of a lysis buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM dithiothreitol, cycloheximide (100 μg/ml), chloramphenicol (100 μg/ml)), and the lysate was treated with 15 U of Turbo DNase (Thermo Fisher Scientific) and then cleared by centrifugation. For RNA-seq, RNA was extracted from the same lysate used for Ribo-seq using Trizol LS (Thermo Fisher Scientific) and Direct-zol RNA Microprep Kit (Zymo Research), then treated with the Human riboPOOL (siTOOLs Biotech) to deplete ribosomal RNAs.
The Ribo-seq library was prepared according to a protocol described previously (Methods 126, 112-129, 2017 and STAR Protoc 1, 100168., 2020). The RNA-seq library was prepared using a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

treatment_protocol: To induce KTN1 expression, cells were treated with 1 μg/ml DOX for 3 days.

value: HeLa

value: KTN1 KO, rescued by dox-inducible KTN1 V2(+)

value: 1 μg/ml dox for 3 days


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(-), Ribo-seq, replicate 2

description:
Library name: Sample15
V4_48_min_2

value: KTN1 KO, rescued by dox-inducible KTN1 V2(-)

value: without dox


title: Rag1-/- ceco-colonic LN_3

value: lymph node


title: ST_7C


title: VCaP cells, Veh, ERG

value: Vehicle


title: ST_7N


title: VCaP cells, DEX, 1 hour, ERG

value: DEX


title: Vitamin A sufficient diet Duodenal LN 1

value: Vitamin A sufficient (control)


title: MCF7_24h_2

city: Hangzhou, Zhejiang 310014, P. R. China.

first: zhuazhua

last: Wu

state: ZheJiang

address: 158 Shangtang Road

department: Center of Oncology, Department of Medical Oncology

institute: Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files including RPKM values for each sample1
Supplementary files format and content: tab-delimited text files including RPKM values for each sample2

source_name: breast cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit

value: breast cancer


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(+), Ribo-seq, replicate 2

description:
Library name: Sample14
V0_3_pls_2


title: Rag1-/- ileum LN_3


title: ST_6T

value: breast cancer tumor


title: Rag1-/- duodenum LN_3


title: Rag1-/- inguinal LN_2


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(+), Ribo-seq, replicate 1

description:
Library name: Sample12
V4_48_pls_1


title: Rag1-/- jejunum LN_3


title: MCF7_6h_4


title: ST_6N

value: Normal breast tumor adjacent

value: post-treatment


title: MCF7_12h_5


title: ST_6C

value: pre-treatment

value: ER+


title: Rag1-/- ceco-colonic LN_2


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(-), Ribo-seq, replicate 1

description:
Library name: Sample11
V4_48_min_1


title: MCF7_Ctr_4


title: Rag1-/- ileum LN_2


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(+), Ribo-seq, replicate 1

description:
Library name: Sample10
V0_3_pls_1


title: ST_5T


title: Rag1-/- jejunum LN_2


title: Cal62-Niraparib, PARP1, Active motif

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Cal-62 cells

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Cal-62 cells

value: thyroid cancer cells

value: PARP1, (Active motif,39561)


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(-), Ribo-seq, replicate 1

description:
Library name: Sample9
V0_3_min_1

value: HeLa


title: ST_5N


title: Rag1-/- duodenum LN_2


title: ST_5C


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(+), RNA-seq, replicate 2

description:
Library name: Sample8
RNA-seq8

data_processing:
Sequence data were processed as previously described but with modifications (Methods 126, 112-129, 2017.). In brief, adapter trimming was performed with fastp v.0.21.0, and reads were mapped to noncoding RNA (ncRNA) sequences with the use of STAR v.2.7.0a to remove reads that originated from rRNA genes and other ncRNA genes in silico. The remaining reads were aligned to the human genome hg38 and assigned to the GENCODE Human release 32 reference from the UCSC Genome Browser (https://genome.ucsc.edu/index.html) with the use of STAR 2.7.0a.
Mapped reads were counted for each Ensembl transcript ID using the GENCODE human reference (release 32)
Assembly: The human genome hg38 and the GENCODE Human release 32 reference
Supplementary files format and content: counts.gene.csv contains raw (unnormalized) read counts at the Ensembl transcript level (one transcript per row). Columns are: (1) Ensembl transcript ID (ENST), (2) transcript length (nt), (3–10) Ribo-seq sample counts, (11–18) RNA-seq sample counts, (19) gene symbol, and (20) gene description.
Supplementary files format and content: The first row contains column headers: V0_3 cells carry the dox-inducible KTN1 V2(−) construct, while V4_48 cells carry the dox-inducible KTN1 V2(−) construct. min indicates DOX(-), while pls indicates DOX(+)

value: KTN1 KO, rescued by dox-inducible KTN1 V2(+)

value: 1 μg/ml dox for 3 days


title: Rag1-/- inguinal LN_1


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(-), Ribo-seq, replicate 2

description:
Library name: Sample13
V0_3_min_2

value: KTN1 KO, rescued by dox-inducible KTN1 V2(-)

value: without dox


title: Cal62-DMSO, PARP1, Active motif

value: PARP1, (Active motif, 39561)


title: ST_1T


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(-), RNA-seq, replicate 2

description:
Library name: Sample7
RNA-seq7


title: ST_1N_B


title: Rag1-/- ceco-colonic LN_1

value: lymph node


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(-), RNA-seq, replicate 2

description:
Library name: Sample5
RNA-seq5


title: Cal62-DMSO, Input


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(+), RNA-seq, replicate 2

description:
Library name: Sample6
RNA-seq6


title: ST_1C


title: B2sh3_IP

first: Junya

last: Ning

state: -- None --

address: Huanhuxi Road, Hexi District, Tianjin

institute: Tianjin Medical University Cancer Institute & Hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: text files include  synthesis analysis of diff.lg.fdr, diff.log2.fc and diff.pvalue of m6A peak in METTL3 knockdown BCPAP cells (A2sh1 and B2sh3) compared with control (A1Ctrl  and B1Ctrl)

source_name: BCPAP

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: BCPAP

value: thyroid cancer cell

value: METTL3 knockdown

tag: rip antibody


title: B2sh3_input


title: Rag1-/- ileum LN_1


title: NBR15_3

source_name: Healthy breast epithelium

value: Healthy breast epithelium

value: No treatment

value: No cancer


title: Cal62-Niraparib, Input


title: NBR15_1


title: Rag1-/- duodenum LN_1


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(-), RNA-seq, replicate 1

description:
Library name: Sample3
RNA-seq3


title: B1Ctrl_IP

value: control


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(+) variant rescue (Cell ID:V4_48), DOX(+), RNA-seq, replicate 1

description:
Library name: Sample4
RNA-seq4


title: NBR14


title: B1Ctrl_input


title: RNA-seq_KO_6h_rep3

city: 上海

first: Zhou-Li

last: Cheng

address: dong'an road 131

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Assembly: mm10
Supplementary files format and content: bigWig

source_name: BMDM

growth_protocol: Bone marrow cells were harvested from the femur and tibia, and differentiated in DMEM (containing 10% fetal calf serum, 1% penicillin–streptomycin and 20 ng/ml M-CSF) for 6 days

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: For RNA-seq, BMDM cells were treated with IFNb for 6h.

value: BMDM

value: Bone Marrow-Derived Macrophage

value: treated with IFNb for 6 hours


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(+), RNA-seq, replicate 1

description:
Library name: Sample2
RNA-seq2

value: HeLa


title: HeLa cells, KTN1 KO, dox-inducible KTN1 V2 exon(-) variant rescue (Cell ID:V0_3), DOX(-), RNA-seq, replicate 1

description:
Library name: Sample1
RNA-seq1


title: A2sh1_input


title: Zebrafish intestinal cells at 5 dpt

city: Rotterdam

first: Wei

last: Zhang

address: Dr. Molewaterplein 40, 3015 GD Rotterdam

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

description:
Library name: LK_ZF_DEAB
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing and generation of the fastq files and filtered counts was performed using cellranger version 4.0.0. Cellranger uses bcl2fastq to perform the demultiplexing step.
Assembly: Danio rerio GRCz10
Supplementary files format and content: Tab-seperated values files and matrix files

organism: Danio rerio

source_name: Intestines

growth_protocol: Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES-buffered E3 medium.

extract_protocol:
At 4 dpf, DEAB treated tg(phox2bb:GFP) zebrafish with a total colonic HSCR phenotype were selected. In total 277 intestines of 5 days post-fertilization (dpf) larvae were isolated, cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single-cell RNA sequencing.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)

treatment_protocol: Tg(phox2bb:GFP) zebrafish embryos were treated with 20 μM DEAB  from 24.5 hpf until 5 dpf.

value: Intestines

value: Primary cells

value: Intestinal cells

value: DEAB


title: HCT116-Steviol+MG132 2

city: JiangSu

first: Zhang Meiqi

address: 59 Cangwu Road, Haizhou District, Lianyungang City

institute: 江苏海洋大学

description: Library name: Sample8

data_processing:
Raw data quality assessed with FastQC.
Quality trimming using Trimmomatic.
Alignment with HISAT2.
Redundancy and insertion fragment distribution analysis with RSeQC.Uniformity and genome structure distribution analysis with Qualimap.
Gene coverage and sequencing distribution analysis with BEDTools.
Assembly: HISAT2
Supplementary files format and content: The counts matrices provide gene expression counts across different samples. RSEM quantification files contain estimated expression levels for each gene and transcript. Quality control reports from FastQC are also included to visualize and assess the sequencing data quality.

source_name: Colorectal Carcinoma

growth_protocol: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 80µM Steviol drug,one group was treated with 2µM MG132 drug one group was treated with 2µM MG132+ drug 80µM Steviol drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: Colorectal Carcinoma

value: Colorectal cells

value: WT

value: Steviol, 80 μM, + MG132, 2 μM,24 hours


title: RNA-seq_KO_6h_rep1


title: LX-2 cells, transfected with NSUN2 SiRNA,TGF-β24h,SiNSUN2_TGFB_3

city: Wuhan

first: An

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

description:
Library name: SiNSUN2_TGFB_3
Transcriptome profile of LX-2 cells transfected with NSUN2 SiRNA and treated with human recombinant TGF beta,,biological rep3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Rawdata (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome.
Assembly: hg38
Supplementary files format and content: CSV file includes raw counts for each Sample
Supplementary files format and content: CSV file includes FPKM values for each Sample

growth_protocol: LX-2 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and  1% antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was harvested using TRIzol reagent, and a minimum of 2 μg of total RNA per sample was used for the construction of sequencing libraries .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LX-2 was stimulated by 5ng/ml TGF-β1 (PeproTech, USA) and after 24 hours we extracted the total RNA. siRNA specific to NSUN2 was transfected into cells using Lipofectamine 2000 (Invitrogen, USA).After 48 hours of transfection,the cells were treated with 5ng/ml of TGF-β1 and after 24 hours we extracted the total RNA.

value: hepatic stellate cells

value: transfected with NSUN2 SiRNA and treated with human recombinant TGF-β1


title: Rag1-/- jejunum LN_1

value: lymph node


title: A1Ctrl_IP

value: BCPAP

value: thyroid cancer cell


title: HCT116-Steviol+MG132 1

description: Library name: Sample7

extract_protocol:
One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer.
Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).


title: LX-2 cells, transfected with NSUN2 SiRNA,TGF-β24h,SiNSUN2_TGFB_2

description:
Library name: SiNSUN2_TGFB_2
Transcriptome profile of LX-2 cells transfected with NSUN2 SiRNA and treated with human recombinant TGF beta,,biological rep2


title: A1Ctrl_input

value: control


title: HCT116-MG132 2

description: Library name: Sample6

value: MG132, 2 μM, 24 hours


title: LX-2 cells, transfected with NSUN2 SiRNA,TGF-β24h,SiNSUN2_TGFB_1

description:
Library name: SiNSUN2_TGFB_1
Transcriptome profile of LX-2 cells transfected with NSUN2 SiRNA and treated with human recombinant TGF beta,,biological rep1


title: RNA-seq_WT_6h_rep1

value: BMDM

value: Bone Marrow-Derived Macrophage

value: treated with IFNb for 6 hours


title: HCT116-MG132 1

description: Library name: Sample5


title: A2sh1_IP

value: METTL3 knockdown


title: LX-2 cells, transfected with NSUN2 SiRNA,SiNSUN2_3

description:
Library name: SiNSUN2_3
Transcriptome profile of LX-2 cells transfected with NSUN2 SiRNA,biological rep3

value: transfected with NSUN2 SiRNA


title: RNA-seq_KO_6h_rep2


title: Niraparib treatment replication 1

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to mm10 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: Excel file includes Normalized count values for each Sample.

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: thyroid cancer cells

value: Niraparib


title: Niraparib treatment replication 2


title: RNA-seq_KO_0h_rep3

value: treated with PBS for 6 hours


title: DMSO treatment replication 2

value: DMSO


title: HCT116-Steviol2

description: Library name: Sample4

value: Colorectal Carcinoma

value: Colorectal cells

value: WT

value: Steviol, 80 μM, 24 hours


title: HCT116-Steviol1

description: Library name: Sample3


title: RNA-seq_KO_0h_rep2


title: LX-2 cells, transfected with NSUN2 SiRNA,SiNSUN2_2

description:
Library name: SiNSUN2_2
Transcriptome profile of LX-2 cells transfected with NSUN2 SiRNA,biological rep2

value: hepatic stellate cells


title: LX-2 cells, transfected with NSUN2 SiRNA,SiNSUN2_1

description:
Library name: SiNSUN2_1
Transcriptome profile of LX-2 cells transfected with NSUN2 SiRNA,biological rep1


title: DMSO treatment replication 1


title: DMSO-2

description: Library name: Sample2

value: DMSO, 0.1%, 24 hours


title: RNA-seq_KO_0h_rep1


title: ctrl_7

city: Boston

first: Radhika

middle: Sanjay

last: Khetani

state: MA

address: 401 Park Drive, 3rd floor East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
Pseudoalignment with Salmon 0.14.2
Convert from transcript-based counts to gene-based counts with TxImport
Obtain differentially expressed genes and normalized counts with DESeq2 1.30.1
Perform funtional analysis in R with clusterProfiler 3.18.1 and org.Hs.eg.db 3.12.0
Assembly: hg38, ensembl 92
Supplementary files format and content: CSV file with raw counts after TxImport
Supplementary files format and content: CSV file with normalized counts (DESeq2 median of ratios method)

source_name: Intestinal organoid

growth_protocol: see main paper protocol

extract_protocol:
HIOs placed in trizol and homogenized. Extraction using Zymo research RNAextraction
Kapa library prep kit

value: Intestinal organoid

value: GFP-labelled control iPS line

value: intestinal epithelium & mesenchyme


title: DMSO-1

description: Library name: Sample1


title: Donor4_GM2-Pam

city: Amsterdam

first: Nadia

last: van der Meijs

address: De Boelelaan 1108

department: MCBI

institute: Amsterdam UMC

data_processing:
Read and sequence alignment using STAR v2.7.3a
Conversion of SAM files to BAM files using samtools v1.10
featureCounts v2.0.0 was used to quantify aligned reads
Bioconductor/R package DESeq2 v1.44.0 was used for data normalisation using standard settings. Genes with expression lower than 5 counts per million in at least 2 samples were filtered out.
Bioconductor/R package DESeq2 v1.44.0 was used to built a generalised linear model consisting of the donor and treatment to identify the significant differentially expressed genes.
Assembly: Ensemble human genome GRCh38 release 99
Supplementary files format and content: Tab-delimited text file with Normalised counts for each sample

source_name: monocyte-derived dendritic cells

growth_protocol: Human monocytes were differentiated to dendritic cells using rhIL-4 and rhGM-CSF for 4 days.

extract_protocol:
Dendritic cells were washed with PBS and incubated with TRIzol. Total RNA was harvested with a standard TRIzol isolation protocol (Thermo Fisher Scientific, cat#15596018).
1 µg of RNA was used for library preparation using the KAPA mRNA HyperPrep kit (Roche, cat# 08098123702).

treatment_protocol: Differentiated dendritic cells were stimulated with 1µM of a single glycodendrimer or control dendrimer and 5 µg/ml Pam3CysK4 for 5 hrs.

value: monocyte-derived dendritic cells


title: RNA-seq_WT_6h_rep2

value: BMDM

value: Bone Marrow-Derived Macrophage

value: treated with IFNb for 6 hours


title: RNA-seq_WT_0h_rep3


title: ctrl_6


title: RNA-seq_WT_0h_rep2


title: NC-M2

city: taizhou

first: qian

last: zhu

address: gaoxinarea

institute: qian

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

source_name: negative control

extract_protocol:
1 μg total RNA was used for following library preparation.The poly(A) mRNA isolation was performed using Oligo(dT) beads.VV
RNA libraries tor RNA seq were prepared using SMARTER mRNA-Seq Library Prep Kit followng manufacturer's protocols.

value: Peripheral blood

value: macrophages

value: transfected with si-NC


title: MSK_4807C_R1

data_processing:
Gene counts were generated by alignment to human transcriptome GRCh38 using STAR in RSEM.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: txt file with count data from RSEM

source_name: DSRCT

extract_protocol:
Phase separation in OCT frozen tissue lysed in TRIzol was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher catalog # A27828) on the KingFisher Flex Magnetic Particle Processor (Thermo Scientific catalog # 5400630) according to the manufacturer’s protocol
179-700 ng of total RNA with DV200 percentages varying from 3-78% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

value: DSRCT

value: Female

value: Yes


title: ctrl_5


title: FSTL1-M2

source_name: transfected with FSTL1

value: WT

value: transfected with FSTL1


title: Donor4_Forss-Pam

value: Forssman


title: RNA-seq_WT_0h_rep1

value: treated with PBS for 6 hours


title: Donor4_control-Pam

value: control


title: SCC25 cells, DMSO, rep3

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

institute: Southern Medical University

description:
S25_48h_C3
SCC25_JQ1_vs_DMSO.txt

data_processing:
Hisat2 v2.0.5
Clean reads were generated by removing low quality reads and then aligned to the Human Genome Assembly GRCh38/hg38 using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads mapped to each gene, and then the FPKM (Fragments Per Kilobase of sequence per Millions base pairs) of each gene were calculated based on the length of the gene and reads count mapped to the gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was first purified using TRIzol Reagent t and then assessed by 1% agarose gel electrophoresis and the Bioanalyzer 2100 system.
Sequencing libraries were constructed using the NEBNext UltraTM RNA Library Prep Kit for Illumina.

value: Oral squamous cell

value: DMSO

tag: time


title: ctrl_4

value: Intestinal organoid

value: GFP-labelled control iPS line

value: intestinal epithelium & mesenchyme


title: Germ-free inguinal LN_4

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value (adj_pval) < 0.05 were considered significant for downstream analysis
Assembly: mm10
Supplementary files format and content: comma separated variable files for raw counts for each sample
Supplementary files format and content: .tsv files containing kallisto alignment output (estimated counts, TPM, and effective length) for each sample
Supplementary files format and content: .h5 binary files containing run info, abundance esimates, bootstrap estimates, and transcript length information length

source_name: lymph node

treatment_protocol: To identify region-specific gene signatures of gut-draining lymph nodes (LNs) and microbiome role in this, we analyzed duodenum (Duo), jejunum (Jej), ileum (Ile), ceco-colonic (Col) and skin-draining inguinal (Ing, as non-gut reference) LNs RNA from specific pathogen-free (SPF) and germ-free (GF) mice.

value: lymph node

tag: microbes

value: GF

tag: group

value: Germ-free inguinal LN


title: Donor4_BGA-Pam

value: monocyte-derived dendritic cells

value: Blood group A


title: ctrl_3

tag: tissue


title: Vitamin A sufficient Jejunal LN 1

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value (adj_pval) < 0.05 were considered significant for downstream analysis
Assembly: mm10
Supplementary files format and content: comma separated variable files for raw counts for each sample

extract_protocol:
RNA was extracted using TRIZOL protocol, RNA samples were purified using RNAclean XP beads (Beckman Coulter), and RNA concentration was measured with a NanoDrop Microvolume Spectrophotometer (Thermo Fisher).
1000-1500 µg of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

value: female

value: postnatal day 56

value: Vitamin A sufficient (control)


title: SCC25 cells, DMSO, rep2

description:
S25_48h_C2
SCC25_JQ1_vs_DMSO.txt

value: WT


title: Germ-free inguinal LN_3


title: Donor4_aGM2-Pam

value: asialo GM2


title: ctrl_2


title: SCC25 cells, DMSO, rep1

description:
S25_48h_C1
SCC25_JQ1_vs_DMSO.txt


title: Germ-free inguinal LN_2


title: SCC25 cells, JQ1

description:
S25_48h_J3
SCC25_JQ1_vs_DMSO.txt


title: Donor4_GalNac-Pam

value: alfa-GalNAc


title: ctrl_1


title: Germ-free inguinal LN_1


title: Donor3_GalNac-Pam


title: wnt2b_KO_7

value: 517-21 Wnt2b deficient patient iPS line


title: Germ-free ceco-colonic LN_4

value: Germ-free ceco-colonic LN


title: SCC25 cells, JQ1, rep2

description:
S25_48h_J2
SCC25_JQ1_vs_DMSO.txt

value: Oral squamous cell


title: Germ-free ceco-colonic LN_3


title: Donor3_Forss-Pam

value: Forssman


title: wnt2b_KO_6

value: Intestinal organoid


title: Donor3_control-Pam

value: control


title: SCC25 cells, JQ1, rep1

description:
S25_48h_J1
SCC25_JQ1_vs_DMSO.txt


title: wnt2b_KO_5

value: intestinal epithelium & mesenchyme


title: SCC15 cells, DMSO, rep3

description:
S15_48h_C3
SCC15_JQ1_vs_DMSO.txt

value: DMSO


title: Germ-free ceco-colonic LN_2

value: lymph node

value: GF


title: Germ-free ceco-colonic LN_1


title: SCC15 cells, DMSO, rep2

description:
S15_48h_C2
SCC15_JQ1_vs_DMSO.txt


title: wnt2b_KO_3


title: Donor3_aGM2-Pam

value: monocyte-derived dendritic cells


title: SCC15 cells, DMSO, rep1

description:
S15_48h_C1
SCC15_JQ1_vs_DMSO.txt


title: Germ-free ileum LN_4

value: Germ-free ileum LN


title: Donor3_GM2-Pam


title: Donor2_GM2-Pam


title: Germ-free ileum LN_3


title: SCC15 cells, JQ1, rep3

description:
S15_48h_J3
SCC15_JQ1_vs_DMSO.txt


title: Donor2_GalNac-Pam


title: wnt2b_KO_1


title: SCC15 cells, JQ1, rep2

description:
S15_48h_J2
SCC15_JQ1_vs_DMSO.txt


title: Donor2_Forss-Pam


title: Donor2_control-Pam


title: Germ-free ileum LN_1


title: SCC15 cells, JQ1, rep1

description:
S15_48h_J1
SCC15_JQ1_vs_DMSO.txt


title: wnt2b_KO_4


title: Control, 72 hpf, B

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

address: 28645 east hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

description: Library name: control_0_72_B

data_processing:
Reads were mapped and demultiplexed by Alithia Genomics; 88% of reads were mapped to the genome, and 67% were mapped to exons.
Assembly: GRCz12tu
Supplementary files format and content: .csv file containing raw read count data

source_name: Whole Animal

extract_protocol:
RNA extraction was performed using the KingFisher Apex System (ThermoFisher Scientific, Waltham, MA, United States) and Quick-RNA Magbead kit (Zymo Research Corporation, Irvine, CA, United States). Samples were thawed and combined into the homogenization plate (2 mL deep 96-well plate pre-filled with 400 µL 1 mm zirconium silicate beads and 525 µL of lysis buffer) and sealed with a silicone seal. Using the Mini-BeadBeater 96 (BioSpec Products, Bartlesville, OK, United States), the plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 550µL of the supernatant was distributed over two plates, each pre-filled with 275µL of ethanol. Extraction was an automated process that using Mag beads to collect RNA, after a series of washes and treatment with DNase, the RNA is eluted in 50µL of ultra-pure water. RNA quality was assessed using the RNA ScreenTape and the 4200 TapeStation System (Agilent, Santa Clara, CA, United States). The RNA purity was assessed using the 260/230 ratio measured with the Varioskan ALF multimode plate reader (ThermoFisher Scientific, Waltham, MA, United States). RNA concentration was determined using Quant-iT broad-spectrum RNA Reagent and assay kit and Varioskan ALF multimode plate reader (standard curve R2=0.996). The four replicates of each treatment with the highest RNA concentration, which met RNA quality and purity criteria (2.3 ≥ 260/230 ≥ 1.8, RIN=10), were selected for sequencing. The resulting 80 samples were normalized using ultrapure water to the lowest concentration, 56 ng/µL.
library constructuon and RNA sequencing was performed by Alithia Genomics (Epalignes, Switzerland) using their Mercurius™ BRB-SEQ service, which is a multiplexed 3’ RNA sequencing library preparation technique. Samples were sequenced using NextSeq 200 with ~9.6 million reads/sample.

treatment_protocol: All chemicals (8-methylbenzo[a]pyrene, 6-methylbenzo[a]pyrene, and benzo[a]pyrene) were exposed at the same concentrations (0, 0.133, 1.33, and 13.3 µM).  Concentrations were picked that cause no morphological effects (0.133 µM), only x-fin (1.33 µM), and x-fin as well as cranial malformations and edema (13.3 µM). Time points were chosen to be before the observation of any morphological effects (48 hpf) and at the onset of morphological effects (72 hpf). For each chemical and concentration combination, a 96-well plate was exposed, as well as one plate of control embryos.  At 48 and 72 hpf, living embryos were collected at random regardless of morphological phenotypes, and pooled in groups of six. Five replicates of each chemical and concentration combination and control were collected at each time point, pooled sample embryo medium (EM) volume was normalized to 75 µL. Collection plates were placed on ice for one minute, immediately followed by the addition of 100 µL of RNA shield. Plates were sealed with foil seals and kept at -80°C until RNA extraction.

value: Whole Animal

value: 5D WT


title: upf1_3

city: shanghai

first: Yuxin

last: Zhao

address: 2999 north renmin road

institute: Donghua University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: 293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The starvation group was induced by treating the cells with 12 h serum starvation, and the SRSF1, SRPK1, and UPF1 group was induced by treating 12-hour serum starved cells with SRSF1 SRPK1, and UPF1 knockdown.

value: Human renal epithelial cells

value: UPF1 knockdown

value: Serum starvation treatment for 12 h


title: Donor2_BGA-Pam

value: Blood group A


title: Control, 72 hpf, C

description: Library name: control_0_72_C


title: Germ-free jejunum LN_3

city: Philadelphia

first: Aliia

address: 3400 Civic Center Blvd Bldg 421

institute: University of Pennsylvania

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit (Thermo Fisher) according to the manufacturer’s instructions.
1000-1500 ng of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

value: Germ-free jejunum LN


title: Donor2_aGM2-Pam

value: asialo GM2


title: upf1_2


title: upf1_1


title: Germ-free jejunum LN_2


title: Control, 72 hpf, A

description: Library name: control_0_72_A


title: wnt2b_KO_2

value: 517-21 Wnt2b deficient patient iPS line


title: Donor1_GM2-Pam


title: Germ-free duodenum LN_4

value: Germ-free duodenum LN


title: srpk1_3

value: SRPK1 knockdown


title: srpk1_2


title: Germ-free ileum LN_2


title: benzo[a]pyrene, 13.3, 72 hpf, C

description: Library name: benzo_13.3_72_C

value: benzo[a]pyrene


title: Donor1_GalNac-Pam

value: alfa-GalNAc


title: Control, 72 hpf, D

description: Library name: control_0_72_D

value: DMSO


title: Germ-free jejunum LN_4

value: lymph node

value: GF


title: Germ-free duodenum LN_3


title: Donor1_Forss-Pam

value: monocyte-derived dendritic cells

value: Forssman


title: benzo[a]pyrene, 13.3, 72 hpf, B

description: Library name: benzo_13.3_72_B

value: Whole Animal

value: 5D WT


title: srpk1_1

value: Human renal epithelial cells


title: Germ-free duodenum LN_2


title: Germ-free duodenum LN_1


title: Donor1_control-Pam

value: control


title: srsf1_3

value: SRSF1 knockdown

value: Serum starvation treatment for 12 h


title: benzo[a]pyrene, 13.3, 72 hpf, A

description: Library name: benzo_13.3_72_A


title: Donor1_BGA-Pam

value: Blood group A


title: benzo[a]pyrene, 1.33, 72 hpf, D

description: Library name: benzo_1.33_72_D


title: Ex-Germ-free (SPF) inguinal LN_3

value: SPF

value: Ex-Germ-free (SPF) inguinal LN


title: benzo[a]pyrene, 13.3, 72 hpf, D

description: Library name: benzo_13.3_72_D


title: srsf1_2


title: Ex-Germ-free (SPF) inguinal LN_2


title: srsf1_1


title: benzo[a]pyrene, 1.33, 72 hpf, B

description: Library name: benzo_1.33_72_B


title: TM_4μ8C_2

city: Lianyungang

first: yuzien

last: yu

state: Jiangsu

address: 59 Cangwu Road, Haizhou District

department: College of Pharmacy

institute: Jiangsu Ocean University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample

source_name: Liver Cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Liver Cancer

value: Human Liver Cancer Cell


title: TM_4μ8C_1


title: Ex-Germ-free (SPF) inguinal LN_1

last: Fatkhullina


title: sta_2

value: WT


title: Ex-Germ-free (SPF) ceco-colonic LN_4

value: Ex-Germ-free (SPF) ceco-colonic LN


title: benzo[a]pyrene, 1.33, 72 hpf, A

description: Library name: benzo_1.33_72_A

value: benzo[a]pyrene


title: benzo[a]pyrene, 0.133, 72 hpf, D

description: Library name: benzo_0.133_72_D


title: TM_melatonin_2


title: Ex-Germ-free (SPF) ceco-colonic LN_3

value: lymph node


title: TM_melatonin_1


title: sta_1


title: benzo[a]pyrene, 0.133, 72 hpf, C

description: Library name: benzo_0.133_72_C


title: TM_ISRIB_2


title: con_3

value: Serum starvation treatment for 0 h


title: benzo[a]pyrene, 1.33, 72 hpf, C

description: Library name: benzo_1.33_72_C


title: benzo[a]pyrene, 0.133, 72 hpf, B

description: Library name: benzo_0.133_72_B


title: Ex-Germ-free (SPF) ceco-colonic LN_2


title: con_2


title: Ex-Germ-free (SPF) ceco-colonic LN_1


title: benzo[a]pyrene, 0.133, 72 hpf, A

description: Library name: benzo_0.133_72_A


title: TM_ISRIB_1


title: con_1


title: Ex-Germ-free (SPF) ileum LN_4

value: Ex-Germ-free (SPF) ileum LN


title: sta_3


title: TM_MG132_2


title: 6-methylbenzo[a]pyrene, 13.3, 72 hpf, D

description: Library name: 6_13.3_72_D

value: Whole Animal


title: Ex-Germ-free (SPF) ileum LN_3


title: right ventricle,Hic,nine years,duplication 2

city: Chengdu

first: Yuwei

last: Gou

address: No. 211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Hi-C data were preprocessed using the HiC-Pro software (version 3.1.0). In brief, read pairs were aligned to the pig reference genome (Sscrofa 11.1) using BWA (version 11.1.0) with default parameters. We removed reads that could not be aligned to the genome, PCR duplicates or low quality reads (MAPQ < 30). Information for the ratio of intra-chromosomal (cis) or inter-chromosomal (trans) interactions, as well as distance-separated cis interactions can also be obtained using HiC-Pro. Valid read pairs were binned into interaction matrices at 10-Kb, 40-Kb, 100-Kb, and 1-Mb resolutions, and such matrices were normalized by removing intrinsic bias using the Knight-Ruiz (KR) algorithm.
Assembly: sus11
Supplementary files format and content: The file with the suffix. hic records the interaction of each sample genome at 5K, 10K, 20K, 40K, 100K, and 500K resolutions

organism: Sus scrofa

source_name: right ventricle

extract_protocol:
The right ventricle tissue was initially homogenized using liquid nitrogen. Fixation was performed with a 1% formaldehyde solution at room temperature for 10 minutes. Quenching the reaction was achieved using a 0.125 mol/L glycine solution. Samples were suspended in a lysis buffer (composed of 1 mol/L Tris-HCl, 1 mol/L NaCl, 10% CA-630, and protease inhibitors) on ice for 15 minutes. Chromatin was digested with 400 U Mbo I restriction enzyme (NEB) at 37 °C. DNA ends were labeled with biotin and incubated at 37 °C for 45 minutes, followed by enzyme inactivation at a high temperature. DNA ligation was performed by adding T4 DNA ligase (NEB) and incubating for 4-6 hours. After ligation, proteinase K was added to reverse cross-linking during an overnight incubation at 65°C. DNA fragments were purified, dissolved in water, and unligated ends were removed.
Purified DNA fragments were subjected to secondary cutting to control fragment sizes within the range of 350-500 bp. DNA ends were repaired. DNA fragments labeled with biotin were separated using Dynabeads® M-280 Streptavidin (Life Technologies). Constructed Hi-C libraries underwent quality control. Sequencing of the Hi-C libraries was performed using the Illumina NovaSeq 6000 system.

value: right ventricle

value: female

value: nine years


title: 6-methylbenzo[a]pyrene, 13.3, 72 hpf, C

description: Library name: 6_13.3_72_C

value: 5D WT


title: right ventricle,Hic,nine years,duplication 1


title: TM_MG132_1


title: Ex-Germ-free (SPF) ileum LN_2


title: Vitamin A sufficient Ileal LN 2

value: postnatal day 56

value: Vitamin A sufficient (control)


title: TM_DMSO_2


title: 6-methylbenzo[a]pyrene, 13.3, 72 hpf, B

description: Library name: 6_13.3_72_B


title: right ventricle,Hic,6 months postpartum,duplication 2

value: 6 months postpartum


title: Ex-Germ-free (SPF) ileum LN_1

value: SPF


title: TM_DMSO_1

value: Liver Cancer


title: 6-methylbenzo[a]pyrene, 1.33, 72 hpf, D

description: Library name: 6_1.33_72_D


title: 6-methylbenzo[a]pyrene, 1.33, 72 hpf, C

description: Library name: 6_1.33_72_C


title: Ex-Germ-free (SPF) jejunum LN_3

value: Ex-Germ-free (SPF) jejunum LN


title: Ex-Germ-free (SPF) jejunum LN_4


title: TM_2_1

value: Human Liver Cancer Cell


title: ventricle,Hic,Embryo period 70 days,duplication 1

source_name: ventricle

value: ventricle

value: Embryo period 70 days


title: 6-methylbenzo[a]pyrene, 1.33, 72 hpf, B

description: Library name: 6_1.33_72_B


title: TM_1_2


title: Ex-Germ-free (SPF) jejunum LN_2

value: lymph node


title: Ex-Germ-free (SPF) jejunum LN_1


title: Uterus, Mouse3

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

state: CA

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

description:
Library name: Uterus_M3
Column name in csv files: Uterus_M3

data_processing:
Sequencing adaptors were trimmed from raw reads using cutadapt, v1.18 [--no-indels -O 15 -m 15 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC], then UMI’s were extracted using umi_tools [extract --extract-method=string --bc-pattern=NNNNNNN], finally followed by the removal of a single base added during library preparation from the 5’ end using cutadapt [-u -1 -q 10].
Reads were separated into “mature tRNAs” or “tDRs” based on read lengths of >=65 and <65nt, respectively. Reads were subsampled from each tissue sample to account for differences in sequencing depth to 200,000 reads per sample for those >=65nt and 1,000,000 reads per sample for those <65nt using seqtk [sample -s100]. These were then sequentially aligned using bowtie2 [--very-sensitive -k 100] to vector contaminants (UniVec), rRNAs, tRNAs (with the addition of the -CCA tail) identified using tRNAScan-SE (Chan and Lowe 2021), miRNAs from miRbase (Kozomara et al., 2019), snRNAs/snoRNAs/lncRNAs from Ensembl, processed mRNA transcripts (protein_coding) from Ensembl, and lastly to the genome.
Counts associated with these features were then quantified using a custom Python script, choosing the feature annotation with the largest degree of overlap. Multimapping ncRNA reads with more than one highest-scoring alignment were randomly selected.  The resulting count data underwent normalization and differential expression analysis using DESeq2 (Love 2014)
Assembly: GRCm39 (mm11)
Supplementary files format and content: MouseTissue_o65-counts.csv contains raw counts for annotated transcripts using reads >= 65nt in length.
Supplementary files format and content: MouseTissue_u65-counts.csv contains raw counts for annotated transcripts using reads < 65nt in length.

source_name: Uterus

growth_protocol: Tissues were harvested from three 6-8 week old wildtype female C57BL/6J mice at 2-3pm to best account for 12 hr light-dark cycles (7am-7pm light and 7pm-7am dark), which impact gene and protein expression during circadian variations.

extract_protocol:
Total RNA was isolated from ~15-100mg of whole bladder, brain, cecum, distal colon, duodenum, heart, ileum, kidney, liver, lung, mammary gland, ovary, proximal colon, skeletal muscle, skin, spleen, stomach, thymus, and uterus using 1mL of TRI Reagent and a tissue homogenizer, typically yielding ~50-100ug of total RNA.
OTTR-seq

value: Uterus

value: WT

tag: strain


title: TM_1_1


title: Ex-Germ-free (SPF) duodenum LN_4

value: Ex-Germ-free (SPF) duodenum LN


title: 6-methylbenzo[a]pyrene, 1.33, 72 hpf, A

description: Library name: 6_1.33_72_A

value: Whole Animal


title: TM_0.5_2


title: 6-methylbenzo[a]pyrene, 0.133, 72 hpf, D

description: Library name: 6_0.133_72_D


title: 6-methylbenzo[a]pyrene, 13.3, 72 hpf, A

description: Library name: 6_13.3_72_A


title: Uterus, Mouse1

description:
Library name: Uterus_M1
Column name in csv files: Uterus_M1

tag: Sex

value: female


title: TM_0.5_1


title: TM_2_2


title: ventricle,Hic,Embryo period 70 days,duplication 2


title: 6-methylbenzo[a]pyrene, 0.133, 72 hpf, C

description: Library name: 6_0.133_72_C


title: right ventricle,Hic,6 months postpartum,duplication 1

value: right ventricle


title: Duodenal LN MCM_2

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input and normalized using limma/voom (edgeR)
Assembly: mm10
Supplementary files format and content: comma separated variable file for raw counts for each sample
Supplementary files format and content: .tsv files containing kallisto alignment output (estimated counts, TPM, and effective length) for each sample
Supplementary files format and content: comma separated variable file for normalized counts per million (CPM) for each sample

extract_protocol:
Macrophages were sorted into TCL buffer containing 1% 2-mercaptoethanol. RNA was isolated using RNA Clean XP beads (Agentcourt) on a magnetic stand.
cDNA libraries were constructed using Nextera XT Index Kit according to the manufacturer’s protocol.

value: medallury cord macrophages (MCM)


title: Thymus, Mouse2

description:
Library name: Thymus_M2
Column name in csv files: Thymus_M2

source_name: Thymus

value: Thymus


title: 6-methylbenzo[a]pyrene, 0.133, 72 hpf, A

description: Library name: 6_0.133_72_A

value: 5D WT


title: TG_4μ8C_1


title: Stomach, Mouse2

description:
Library name: Stomach_M2
Column name in csv files: Stomach_M2

source_name: Stomach

value: Stomach


title: Ex-Germ-free (SPF) duodenum LN_1

value: SPF


title: Thymus, Mouse1

description:
Library name: Thymus_M1
Column name in csv files: Thymus_M1


title: TG_4μ8C_2

value: Liver Cancer


title: Stomach, Mouse3

description:
Library name: Stomach_M3
Column name in csv files: Stomach_M3


title: 8-methylbenzo[a]pyrene, 13.3, 72 hpf, D

description: Library name: 8_13.3_72_D


title: LPS

city: Shanghai

first: Zixin

last: Wang

address: Siping Road

institute: Tongji University

data_processing:
Sequence reads were trimmed using TrimGalore (v0.6.10).
Trimmed sequence reads were mapped to mm39 using BASAL software v1.8 (https://github.com/JiejunShi/BASAL).
PCR duplicates were removed using sambamba (v1.0.1).
5hmC in CpG contexts was extracted using BASALkit, a tool specifically designed for analyzing alignments generated by BASAL.
High-confidence 5hmC sites (depth ≥ 5) were called using a binomial distribution with p value cut-off of 0.05.
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: ACE-seq

extract_protocol:
DNA extraction was performed following the protocol of Wizard Genomic DNA Purification Kit (Promega). 1. Add 600 μl of Nuclei Lysis Solution, and pipet until no visible cell clumps remain. 2. Add 3 μl of RNase Solution to the nuclear lysate and mix the sample. Incubate the mixture for 30 minutes at 37 °C. 3. Add 200 μl of Protein Precipitation Solution and vortex at high speed for 20 seconds. Chill sample on ice for 5 minutes. 4. Centrifuge for 10 minutes. Carefully remove the supernatant and transfer it to a clean 1.5 ml tube. 5. Add 600 μl isopropanol and gently mix the solution until the white thread-like strands of DNA form a visible mass. 6. Centrifuge for 15 minutes and carefully decant the supernatant. 7. Add 600 μl of 70% ethanol, and gently invert the tube several times to wash the DNA. Centrifuge for 5 minutes. 8. Carefully decant the ethanol and air-dry for 10 minutes. 9. Add 100 μl of DNA Rehydration Solution and incubate at 37 °C for 30 minutes.
Library was constructed following the protocol of EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme). 1. Denature the input DNA into single-stranded DNA at 95 °C for 2 minutes and chill sample on ice for 2 minutes. 2. Add the 3' adapter to the 3' end of the single-stranded DNA at 37 °C for 15 minutes. 3. Extend single-stranded DNA to double-stranded DNA by extension primers. 4. Purify the reaction products using 1.2 × VAHTS DNA Clean Beads. 5. Add the 5' adapter to the 5' end of the double-stranded DNA at 25 °C for 15 minutes. 6. Purify the reaction products using 1 × VAHTS DNA Clean Beads. 7. Amplify DNA library by index primers for 10 cycles. 8. Purify the reaction products using 0.85 × VAHTS DNA Clean Beads. 9. Determine the library concentration by Qubit.

value: BMDM

value: Bone Marrow-Derived Macrophage

value: treated with LPS


title: 6-methylbenzo[a]pyrene, 0.133, 72 hpf, B

description: Library name: 6_0.133_72_B


title: TG_melatonin_2

value: Human Liver Cancer Cell


title: Uterus, Mouse2

description:
Library name: Uterus_M2
Column name in csv files: Uterus_M2


title: TG_melatonin_1


title: aceB

value: treated with aceB[delta] salmonella


title: aceA

value: treated with aceA[delta] salmonella


title: Ex-Germ-free (SPF) duodenum LN_2

value: lymph node


title: Ex-Germ-free (SPF) duodenum LN_3

value: Ex-Germ-free (SPF) duodenum LN


title: TG_ISRIB_2


title: 8-methylbenzo[a]pyrene, 13.3, 72 hpf, C

description: Library name: 8_13.3_72_C

value: Whole Animal


title: TG_ISRIB_1


title: 8-methylbenzo[a]pyrene, 13.3, 72 hpf, A

description: Library name: 8_13.3_72_A


title: Stomach, Mouse1

description:
Library name: Stomach_M1
Column name in csv files: Stomach_M1

value: WT

value: female


title: Spleen, Mouse3

description:
Library name: Spleen_M3
Column name in csv files: Spleen_M3

source_name: Spleen

value: Spleen


title: WT

source_name: BMDM

value: treated with WT salmonella


title: Spleen, Mouse1

description:
Library name: Spleen_M1
Column name in csv files: Spleen_M1


title: 8-methylbenzo[a]pyrene, 13.3, 72 hpf, B

description: Library name: 8_13.3_72_B

value: 5D WT


title: NC

value: treated with PBS


title: 8-methylbenzo[a]pyrene, 1.33, 72 hpf, D

description: Library name: 8_1.33_72_D


title: TG_MG132_2


title: TG_MG132_1


title: Skin, Mouse3

description:
Library name: Skin_M3
Column name in csv files: Skin_M3

source_name: Skin

value: Skin


title: 8-methylbenzo[a]pyrene, 1.33, 72 hpf, C

description: Library name: 8_1.33_72_C


title: RNA-seq_HI+G_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: For RNA-seq, BMDM cells were treated with different S. Tm strains for indicated time.

value: treated with heat-killed salmonella and glyoxylate for 18 hours


title: Skin, Mouse2

description:
Library name: Skin_M2
Column name in csv files: Skin_M2


title: RNA-seq_HI+G_rep3

value: BMDM


title: 8-methylbenzo[a]pyrene, 1.33, 72 hpf, B

description: Library name: 8_1.33_72_B


title: TG_DMSO_2

value: Liver Cancer

value: DMSO


title: TG_DMSO_1

value: Human Liver Cancer Cell


title: SkeletalMuscle, Mouse3

description:
Library name: SkeletalMuscle_M3
Column name in csv files: SkeletalMuscle_M3

source_name: SkeletalMuscle

value: SkeletalMuscle


title: RNA-seq_HI+G_rep1

value: Bone Marrow-Derived Macrophage


title: 8-methylbenzo[a]pyrene, 1.33, 72 hpf, A

description: Library name: 8_1.33_72_A


title: RNA-seq_HI_rep2

value: treated with heat-killed salmonella for 18 hours


title: TG_2_1


title: Skin, Mouse1

description:
Library name: Skin_M1
Column name in csv files: Skin_M1


title: TG_2_2


title: 8-methylbenzo[a]pyrene, 0.133, 72 hpf, C

description: Library name: 8_0.133_72_C


title: RNA-seq_HI_rep3


title: SkeletalMuscle, Mouse1

description:
Library name: SkeletalMuscle_M1
Column name in csv files: SkeletalMuscle_M1


title: SkeletalMuscle, Mouse2

description:
Library name: SkeletalMuscle_M2
Column name in csv files: SkeletalMuscle_M2


title: TG_1_2


title: RNA-seq_HI_rep1


title: 8-methylbenzo[a]pyrene, 0.133, 72 hpf, B

description: Library name: 8_0.133_72_B


title: 8-methylbenzo[a]pyrene, 0.133, 72 hpf, D

description: Library name: 8_0.133_72_D


title: ProximalColon, Mouse3

description:
Library name: ProximalColon_M3
Column name in csv files: ProximalColon_M3

source_name: ProximalColon

value: ProximalColon


title: RNA-seq_WT_rep3

value: treated with WT salmonella for 18 hours


title: TG_1_1


title: ProximalColon, Mouse2

description:
Library name: ProximalColon_M2
Column name in csv files: ProximalColon_M2

value: WT


title: 8-methylbenzo[a]pyrene, 0.133, 72 hpf, A

description: Library name: 8_0.133_72_A

value: Whole Animal


title: TG_0.5_2


title: RNA-seq_WT_rep2


title: Control, 48 hpf, D

description: Library name: control_0_48_D


title: ProximalColon, Mouse1

description:
Library name: ProximalColon_M1
Column name in csv files: ProximalColon_M1

value: female


title: Control, 48 hpf, C

description: Library name: control_0_48_C


title: Ovary, Mouse3

description:
Library name: Ovary_M3
Column name in csv files: Ovary_M3

source_name: Ovary

value: Ovary


title: FCCP_3_MA_2


title: Control, 48 hpf, B

description: Library name: control_0_48_B

value: 5D WT


title: TG_0.5_1


title: FCCP_3_MA_1


title: RNA-seq_NC_rep2

value: treated with PBS for 18 hours


title: Control, 48 hpf, A

description: Library name: control_0_48_A


title: Ovary, Mouse2

description:
Library name: Ovary_M2
Column name in csv files: Ovary_M2


title: Ovary, Mouse1

description:
Library name: Ovary_M1
Column name in csv files: Ovary_M1


title: benzo[a]pyrene, 13.3, 48 hpf, D

description: Library name: benzo_13.3_48_D

value: benzo[a]pyrene


title: MammaryGland, Mouse3

description:
Library name: MammaryGland_M3
Column name in csv files: MammaryGland_M3

source_name: MammaryGland

value: MammaryGland


title: RNA-seq_NC_rep1

value: BMDM


title: pCI_23

city: Kunming

first: Yifei

last: Dong

state: Yunnan Province

address: No. 374, Dian Burma Avenue

institute: Dept. of Rehabilitation, The 2st Affiliated Hospital of Kunming Medical University

description: experimental,replicate biosample 6

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: mm10
Supplementary files format and content: tab-delimited text files include GENE count for each Sample

source_name: Brain

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: Brain

value: pCI


title: RNA-seq_NC_rep3


title: RNA-seq_WT_6h_rep3

value: treated with IFNb for 6 hours


title: benzo[a]pyrene, 13.3, 48 hpf, C

description: Library name: benzo_13.3_48_C


title: FCCP_MG132_2

value: Liver Cancer

value: Human Liver Cancer Cell


title: MammaryGland, Mouse2

description:
Library name: MammaryGland_M2
Column name in csv files: MammaryGland_M2


title: pCI_30

description: experimental,replicate biosample 5


title: FCCP_DMSO_2


title: RNA-seq_WT_rep1

value: Bone Marrow-Derived Macrophage


title: benzo[a]pyrene, 13.3, 48 hpf, B

description: Library name: benzo_13.3_48_B


title: pCI_37

description: experimental,replicate biosample 4


title: FCCP_DMSO_1


title: Lung, Mouse3

description:
Library name: Lung_M3
Column name in csv files: Lung_M3

source_name: Lung

value: Lung


title: pCI_44

description: experimental,replicate biosample 3


title: FCCP_5_1


title: Lung, Mouse2

description:
Library name: Lung_M2
Column name in csv files: Lung_M2


title: pCI_45

description: experimental,replicate biosample 2


title: Lung, Mouse1

description:
Library name: Lung_M1
Column name in csv files: Lung_M1


title: FCCP_5_2


title: pCI_51

description: experimental,replicate biosample 1


title: Liver, Mouse3

description:
Library name: Liver_M3
Column name in csv files: Liver_M3

source_name: Liver

value: Liver


title: FCCP_2.5_2


title: tCI_24

description: control, replicate biosample 6

value: tCI


title: FCCP_MG132_1


title: benzo[a]pyrene, 1.33, 48 hpf, B

description: Library name: benzo_1.33_48_B

source_name: Whole Animal

value: Whole Animal


title: benzo[a]pyrene, 1.33, 48 hpf, A

description: Library name: benzo_1.33_48_A


title: FCCP_2.5_1

source_name: Liver Cancer


title: FCCP_1.25_2


title: MammaryGland, Mouse1

description:
Library name: MammaryGland_M1
Column name in csv files: MammaryGland_M1

value: WT

value: female


title: benzo[a]pyrene, 13.3, 48 hpf, A

description: Library name: benzo_13.3_48_A

value: 5D WT


title: FCCP_1.25_1


title: benzo[a]pyrene, 0.133, 48 hpf, D

description: Library name: benzo_0.133_48_D


title: tCI_35

description: control, replicate biosample 4


title: benzo[a]pyrene, 0.133, 48 hpf, C

description: Library name: benzo_0.133_48_C


title: Kidney, Mouse3

description:
Library name: Kidney_M3
Column name in csv files: Kidney_M3

source_name: Kidney

value: Kidney


title: Donor3_BGA-Pam

source_name: monocyte-derived dendritic cells

value: monocyte-derived dendritic cells

value: Blood group A


title: benzo[a]pyrene, 1.33, 48 hpf, D

description: Library name: benzo_1.33_48_D

value: benzo[a]pyrene


title: benzo[a]pyrene, 1.33, 48 hpf, C

description: Library name: benzo_1.33_48_C


title: tCI_40

description: control, replicate biosample 3

value: Brain


title: HK-2 cells,  TGFb and FT895, 12h, rep3

city: Shenzhen

first: Han

last: Wu

address: Liuxian Road 1066

institute: Shenzhen University

data_processing:
Based on the sequencing by synthesis (SBS) technology, the Illumina high-throughput sequencing platform sequences the cDNA library.
Remove low-quality reads (including removing reads with an N ratio > 10%; removing reads with a quality value Q≤10 and a base number that accounts for more than 50% of the entire read)
Sequence reads were mapped to reference genome GRCh38 using HISAT2 software.
The StringTie algorithm normalizes the number of mapped reads and transcript length in the sample. FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) is used as an indicator to measure the expression level of transcripts or genes.
Assembly: StringTie to assemble and quantify the reads on the alignment.
Supplementary files format and content: Excel file include RPKM values for each sample.

source_name: HK-2 cells

growth_protocol: HK-2 cells were cultured in DMEM/F12 containing 10% fetal bovine serum  and 1% penicillin and streptomycin.

extract_protocol:
Total RNA from 1 × 10^7 cells was isolated by Trizol extraction with DNase I treatment for each sample.
RNA-seq library preparation and sequencing on an Illumina platform were finished by BMK Inc (Beijing, China).

treatment_protocol: HK-2 cells treated with 2 ug/ml TGFβ with the presence of HDAC11 inhibitor FT895 or vehicle (DMSO) for 1 h or 12 h.  Equal volume of PBS treated cells were serve as mock control.

value: HK-2 cells

value: Epithelial  cells

value: TGFb and FT895, 12h


title: benzo[a]pyrene, 0.133, 48 hpf, B

description: Library name: benzo_0.133_48_B


title: tCI_48

description: control, replicate biosample 2


title: Kidney, Mouse2

description:
Library name: Kidney_M2
Column name in csv files: Kidney_M2


title: benzo[a]pyrene, 0.133, 48 hpf, A

description: Library name: benzo_0.133_48_A


title: HK-2 cells,  TGFb and FT895, 12h, rep2


title: tCI_52

description: control, replicate biosample 1


title: Liver, Mouse2

description:
Library name: Liver_M2
Column name in csv files: Liver_M2


title: Kidney, Mouse1

description:
Library name: Kidney_M1
Column name in csv files: Kidney_M1


title: HK-2 cells,  TGFb and FT895, 12h, rep1


title: HK-2 cells, TGFb, 12h, rep3

value: TGFb, 12h


title: 6-methylbenzo[a]pyrene, 13.3, 48 hpf, D

description: Library name: 6_13.3_48_D


title: Ileum, Mouse3

description:
Library name: Ileum_M3
Column name in csv files: Ileum_M3

source_name: Ileum

value: Ileum


title: pancreas, exercise, 3

city: Ruian

first: Wenya

last: Weng

state: Zhejiang

address: Room 1204, Science and Education Building, No. 168 Ruifeng Avenue, Anyang Street,

institute: the Third affliated hospital of Wenzhou medical University

description: diabetic-Exercise

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger software (v7.1.0)
Assembly: Mus musculus Ensembl V105
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
pancreas were dissociated into single cells by dissociation solution.
Single-cell libraries were built by using the 10x Chromium platform(10x Genomics) 3-prime kit(V3).

value: pancreas

value: diabetic-Exercise


title: tCI_28

description: control, replicate biosample 5

value: tCI


title: 6-methylbenzo[a]pyrene, 13.3, 48 hpf, C

description: Library name: 6_13.3_48_C

value: Whole Animal


title: Liver, Mouse1

description:
Library name: Liver_M1
Column name in csv files: Liver_M1

value: Liver

value: WT


title: Ileum, Mouse2

description:
Library name: Ileum_M2
Column name in csv files: Ileum_M2

value: female


title: pancreas,seden, 3

description: diabetic

value: diabetic


title: 6-methylbenzo[a]pyrene, 13.3, 48 hpf, B

description: Library name: 6_13.3_48_B

value: 5D WT


title: HK-2 cells, TGFb, 12h, rep2


title: Heart, Mouse3

description:
Library name: Heart_M3
Column name in csv files: Heart_M3

source_name: Heart

value: Heart


title: pancreas, seden, 3


title: HK-2 cells,  TGFb and FT895, 1h, rep3

value: TGFb and FT895, 1h


title: HK-2 cells, TGFb, 12h, rep1


title: 6-methylbenzo[a]pyrene, 13.3, 48 hpf, A

description: Library name: 6_13.3_48_A


title: HK-2 cells,  TGFb and FT895, 1h, rep2


title: 6-methylbenzo[a]pyrene, 1.33, 48 hpf, D

description: Library name: 6_1.33_48_D


title: 6-methylbenzo[a]pyrene, 1.33, 48 hpf, C

description: Library name: 6_1.33_48_C


title: Heart, Mouse1

description:
Library name: Heart_M1
Column name in csv files: Heart_M1


title: HK-2 cells,  TGFb and FT895, 1h, rep1


title: MPTA_1

city: Nanjing

first: Yuzhuo

last: Xu

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Assembly: GRCm39
Supplementary files format and content: xls files include counts and tpm values for each sample

source_name: mouse embryonic stem cell

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mouse embryonic stem cell

value: Mpp8/Tasor dko


title: Heart, Mouse2

description:
Library name: Heart_M2
Column name in csv files: Heart_M2


title: Duodenum, Mouse3

description:
Library name: Duodenum_M3
Column name in csv files: Duodenum_M3

source_name: Duodenum

value: Duodenum


title: 6-methylbenzo[a]pyrene, 1.33, 48 hpf, B

description: Library name: 6_1.33_48_B


title: WT_3


title: MPTA_3


title: MPTA_2


title: HK-2 cells, TGFb, 1h, rep3

value: HK-2 cells

value: Epithelial  cells

value: TGFb, 1h


title: Duodenum, Mouse2

description:
Library name: Duodenum_M2
Column name in csv files: Duodenum_M2


title: 6-methylbenzo[a]pyrene, 1.33, 48 hpf, A

description: Library name: 6_1.33_48_A


title: WT_2


title: 6-methylbenzo[a]pyrene, 0.133, 48 hpf, D

description: Library name: 6_0.133_48_D


title: HK-2 cells, TGFb, 1h, rep2


title: Duodenum, Mouse1

description:
Library name: Duodenum_M1
Column name in csv files: Duodenum_M1


title: Ileum, Mouse1

description:
Library name: Ileum_M1
Column name in csv files: Ileum_M1

value: Ileum


title: HK-2 cells, TGFb, 1h, rep1


title: Donor1_aGM2-Pam

data_processing:
Read and sequence alignment using STAR v2.7.3a
Conversion of SAM files to BAM files using samtools v1.10
featureCounts v2.0.0 was used to quantify aligned reads
Bioconductor/R package DESeq2 v1.44.0 was used for data normalisation using standard settings. Genes with expression lower than 5 counts per million in at least 2 samples were filtered out.
Bioconductor/R package DESeq2 v1.44.0 was used to built a generalised linear model consisting of the donor and treatment to identify the significant differentially expressed genes.
Assembly: Ensemble human genome GRCh38 release 99
Supplementary files format and content: Tab-delimited text file with Normalised counts for each sample

extract_protocol:
Dendritic cells were washed with PBS and incubated with TRIzol. Total RNA was harvested with a standard TRIzol isolation protocol (Thermo Fisher Scientific, cat#15596018).
1 µg of RNA was used for library preparation using the KAPA mRNA HyperPrep kit (Roche, cat# 08098123702).

value: monocyte-derived dendritic cells

value: asialo GM2


title: 6-methylbenzo[a]pyrene, 0.133, 48 hpf, C

description: Library name: 6_0.133_48_C

value: Whole Animal


title: DistalColon, Mouse3

description:
Library name: DistalColon_M3
Column name in csv files: DistalColon_M3

source_name: DistalColon

value: DistalColon


title: HK-2 cells, mock, 0h, rep3

value: WT

value: Untreat control


title: 6-methylbenzo[a]pyrene, 0.133, 48 hpf, B

description: Library name: 6_0.133_48_B


title: DistalColon, Mouse2

description:
Library name: DistalColon_M2
Column name in csv files: DistalColon_M2

value: female