title: peripheral blood, colorectal cancer-r1 (JGA0013)

value: M

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (JGA0018)

status: Public on Aug 31 2024

type: RNA

city: Richmond

first: Adam

last: Dempsey

state: VA

address: 8751 Park Central Drive, Suite 200

country: USA

institute: StageZero Life Sciences

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 4, Affymetrix).

extract_protocol: Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.

treatment_protocol: Blood plasma was removed after centrifugation and a hypotonic buffer was added at a 3:1 volume ratio to lyse the red blood cells. The mixture was centrifuged to yield a pellet for subsequent total RNA isolation.

tag: tissue

value: peripheral blood

tag: gender

tag: age

tag: cancer dx


title: defb_causp_m_het_4_5

type: SRA

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

description:
m_het_4_5_S56
Supplemental_Table_S6_7.xlsx

library_source: transcriptomic

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

molecule: polyA RNA

organism: Mus musculus

source_name: preimplantation embryo

extract_protocol:
RNA was isolated using RNA-Clean XP beads
Illumina Nextera XT Kit

value: preimplantation embryo

tag: developmental stage

value: Morula

tag: fvb/nj donor egg fertilized by

value: Dgcr8+/fl; Defb41-iCre cauda sperm

tag: genome build


title: peripheral blood, colorectal cancer-r1 (FS0005)

value: F


title: peripheral blood, colorectal cancer-r1 (JH0047)


title: 5xFAD, Vehicle-treated, male, microglia 3

city: Sacramento

first: Jacopo

last: Di Lucente

state: CA

address: 2805 50th Street

department: Pathology and Laboratory Medicine

institute: UC Davis

description: Vehicle 3

data_processing:
Glaxy version 24.0.3
Sequence reads were trimmed Trimmomatic (version 0.39)
Trimmed reads were allign to mm10 using HISAT2 (version 2.2.1)
Gene expression was measured using featureCounts (version 2.0.3)
Differentially expressed features were determined using DESeq2 (version 2.11.40.8)
Assembly: mm10
Supplementary files format and content: Normalized counts

source_name: brain

extract_protocol:
RNA was harvested using Rneasy plus universal mini kit (quiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Following is the workflow of library construction. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: brain

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: Vehicle


title: peripheral blood, colorectal cancer-r1 (JGA0004)


title: peripheral blood, colorectal cancer-r1 (DS0003)


title: defb_causp_m_het_4_4

description:
m_het_4_4_S55
Supplemental_Table_S6_7.xlsx


title: Normal thyroid tissue, Patient 12: Adults, 64-year-old female, ND5

city: Fuzhou

first: Bo Wang

last: Wang

state: Fujian province

address: 29 XinQuan Rd

department: Department of Thyroid and Parathyroid Surgery

country: China

institute: Fujian Medical University Union Hospital

library_source: transcriptomic single cell

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through in-hous eperl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q3 0 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired- end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selectedHisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level. The raw counts were first normalized using TPM (Zhou et al., 2010) Normalized expression level = (readCount*1,000,000) / libsize (libsize is the sum of circRNA readcount).
For the samples without biological replicates. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold fbr significantly differential expression
Assembly: GRCh38.p14
Supplementary files format and content: Text file include FRKM values for each sample.

source_name: Normal thyroid tissue

extract_protocol:
Ribosomal RNA was removed by Epicentre Ribozer rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA.
The sequencing libraries were generated by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370-420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). The Qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy, according to effective library concentration and data amount required.

value: Normal thyroid tissue

value: female

tag: histological type


title: Normal thyroid tissue, Patient 8: Adults, 38-year-old male, ND1

value: male


title: 5xFAD, Vehicle-treated, male, microglia 2

description: Vehicle 2


title: Normal thyroid tissue, Patient 5: Young Adult, 28-year-old male, NY5


title: defb_causp_m_het_4_3

description:
m_het_4_3_S54
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_het_4_7

description:
m_het_4_7_S62
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (AN4019)


title: 5xFAD, Vehicle-treated, male, microglia 1

description: Vehicle 1


title: defb_causp_m_het_4_2

description:
m_het_4_2_S53
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (AN0014)


title: Normal thyroid tissue, Patient 3: Young Adult, 25-year-old male, NY3


title: Normal thyroid tissue, Patient 9: Adults, 43-year-old female, ND2


title: defb_causp_m_het_4_1

description:
m_het_4_1_S63
Supplemental_Table_S6_7.xlsx


title: BSF_pT_TTPY_1

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

data_processing:
Reads were mapped with STAR v2.7.10b
Featurecounts were done with FeatureCounts from the package Subread v2.0.4
Assembly: TriTrypDB-63_TbruceiLister427_2018 from https://tritrypdb.org/
Supplementary files format and content: Tab delimited tables with Read Count data

organism: Trypanosoma brucei

source_name: Lister 427

growth_protocol: Bloodstream forms of T. brucei brucei “single marker” S427 (S16) (Lister 427, antigenic type MiTat 1.2, clone 221a) were grown at 37 °C, 5% CO2 in HMI-9 medium supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen, EEUU); Procyclic forms of T. brucei 449 were cultured at 28°C, 5% CO2 in SDM-79 medium containing 10% hiFBS (Invitrogen, EEUU) and 7.5 μg ml−1 hemin (Sigma-Aldrich, EEUU).

extract_protocol:
Total RNA was purified using a total RNA isolation kit (Qiagen, Germany)
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: T. brucei parasites in logarithmic phase were incubated with 2X of the half-maximal inhibitory concentration of AQ1 (BSF: 0,24 uM and PCF: 9), Pt-TTPY (BSF: 0,26 uM and PCF: 48,46 uM) and pyridostatin (BSF: 11,04 uM and PCF: 18,18 uM) for 18 h at 37ºC or 28 ºC,  5% CO2 and 100% of humidity

tag: strain

value: Lister 427

value: BCF


title: BSF_pT_TTPY_2


title: peripheral blood, colorectal cancer-r1 (DC3005)


title: Thyroid carcinoma, Patient 12: Adults, 64-year-old female, AD5

source_name: Thyroid carcinoma

value: Thyroid carcinoma

value: Papillary Thyroid Carcinoma

tag: primary neoplasm_focus_type

value: Unifocal

tag: invasion-related cancer_type

value: Invasion-related Cancer


title: Thyroid carcinoma, Patient 13: Adults, 66-year-old female, AD6


title: defb_causp_m_het_3_7

description:
m_het_3_7_S37
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (AN0011)

value: peripheral blood

value: M

value: colorectal cancer


title: Thyroid carcinoma, Patient 11: Adults, 63-year-old female, AD4


title: defb_causp_m_het_3_6

description:
m_het_3_6_S36
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: Morula

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: Normal thyroid tissue, Patient 4: Young Adult, 26-year-old female, NY4


title: BSF_AQ1_2


title: Thyroid carcinoma, Patient 10: Adults, 43-year-old female, AD3


title: defb_causp_m_het_3_8

description:
m_het_3_8_S5
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_het_3_5

description:
m_het_3_5_S35
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_het_3_4

description:
m_het_3_4_S34
Supplemental_Table_S6_7.xlsx


title: Thyroid carcinoma, Patient 9: Adults, 43-year-old female, AD2


title: BSF_AQ1_1


title: BSF_Pyrid_1

value: Pyrid


title: BSF_wt_2

value: wt


title: Thyroid carcinoma, Patient 8: Adults, 38-year-old male, AD1

value: Non-Invasion-related Cancer


title: BSF_Pyrid_2


title: defb_causp_m_het_3_3

description:
m_het_3_3_S33
Supplemental_Table_S6_7.xlsx


title: PCF_Pyrid_2

value: PCF


title: defb_causp_m_het_3_2

description:
m_het_3_2_S32
Supplemental_Table_S6_7.xlsx


title: Thyroid carcinoma, Patient 7: Young Adult, 29-year-old female, AYA7

value: female


title: Thyroid carcinoma, Patient 6: Young Adult, 28-year-old female, AYA6


title: defb_causp_m_het_2_8

description:
m_het_2_8_S22
Supplemental_Table_S6_7.xlsx


title: PCF_Pyrid_1

value: Lister 427


title: peripheral blood, colon polyps-r1 (RC801)

value: colon polyps


title: defb_causp_m_het_2_7

description:
m_het_2_7_S21
Supplemental_Table_S6_7.xlsx


title: Thyroid carcinoma, Patient 5: Young Adult, 28-year-old male, AYA5

value: Thyroid carcinoma

value: male

value: Multifocal


title: defb_causp_m_het_2_6

description:
m_het_2_6_S20
Supplemental_Table_S6_7.xlsx


title: Thyroid carcinoma, Patient 4: Young Adult, 26-year-old female, AYA4

value: Papillary Thyroid Carcinoma


title: Thyroid carcinoma, Patient 3: Young Adult, 25-year-old male, AYA3

value: Unifocal

value: Invasion-related Cancer


title: defb_causp_m_het_2_5

description:
m_het_2_5_S19
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC779)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood

value: M


title: peripheral blood, colon polyps-r1 (RC783)


title: peripheral blood, colon polyps-r1 (RC722)


title: PCF_pT_TTPY_1


title: peripheral blood, colon polyps-r1 (RC772)

value: F


title: peripheral blood, colon polyps-r1 (RC684p)


title: peripheral blood, colon polyps-r1 (RC758)


title: peripheral blood, colon polyps-r1 (RC755)


title: peripheral blood, colon polyps-r1 (RC646)


title: peripheral blood, colon polyps-r1 (RC630)


title: peripheral blood, colon polyps-r1 (RC632)


title: peripheral blood, colon polyps-r1 (RC751)


title: defb_causp_m_het_2_4

description:
m_het_2_4_S18
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: Morula

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: PCF_AQ1_2


title: Thyroid carcinoma, Patient 2: Young Adult, 20-year-old female, AYA2


title: PCF_pT_TTPY_2


title: defb_causp_m_het_2_3

description:
m_het_2_3_S17
Supplemental_Table_S6_7.xlsx


title: PCF_wt_2

value: wt


title: Thyroid carcinoma, Patient 1: Adolescent, 9-year-old female, AYA1


title: peripheral blood, colon polyps-r1 (RC715p)


title: defb_causp_m_het_2_2

description:
m_het_2_2_S23
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_het_1_3

description:
m_het_1_3_S3
Supplemental_Table_S6_7.xlsx


title: Sample_Panc1_319

city: Kansas City

first: Michael

last: VanSaun

state: KS

address: 3901 Rainbow Blvd

institute: The University of Kansas Medical Center

description: treated with hAT-CM from patient 5929-600319

data_processing:
For each sample, quality-control was conducted by using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Samples that passed quality-control were aligned to human-genome-hg38 with RSEM (33) and bowtie2 (34). Counts were used for downstream analysis. Prior to DE analysis, non-expressed genes (genes having low:zero counts) were filtered out to remove biologically uninteresting genes, and attenuate the burden of multiple-testing. DE-analyses among groups were carried out using a generalized-linear-model based on negative binomial distribution in edgeR. Pairwise-comparisons were carried out by specifying appropriate contrast statements in the modeling framework. Multiple-testing adjustments were carried out using Benjamini-Hochberg’s False-Discovery-Rate method. Volcano plots were made from each comparison.
Assembly: Samples that passed quality-control were then aligned to the human genome (hg38) with RSEM and bowtie2.
Supplementary files format and content: Normalized counts
Supplementary files format and content: Excel worksheet

source_name: Pancreas

growth_protocol: Cell lines were trypsinized using 0.25% Trypsin-EDTA [Gibco™#25200056] from 10cm2 culture dishes, then neutralized with complete media once detached from the plate. Cells were counted, pelleted at 300xg for 5 minutes, then resuspended in complete media and distributed at 1E6/well in a 6-well plate.

extract_protocol:
Cells were cultured 24 hours, washed 2x with 1mL of ice-cold PBS [Sera-Care 5460-0023], then lysed in 300μL QIA-zol [Qiagen#51-13-02]. RNA was extracted using Direct-zol RNA Miniprep Kit [Zymo Research#R2052] following the manufacturer’s protocol.
Library prep was completed following Tecan Universal Plus mRNA library Prep (Stranded mRNA Library), then sequenced on a NovaSeq S1-200 cycle (100PE) flow cell using XP 2-lane chemistry for independent lane loading.  A second sequencing run was used to provide supplemental reads for samples HPNE_297 & HPNE_415. A second set of experiments were combined as more patient samples were accrued. Groupings of samples were MiaPaCa2, Panc1, and HPNE-G12D.

treatment_protocol: The next day, cells were washed 2x with SF-DMEM, then treated with either SF-DMEM+Anti-Anti, or individual-patient hAT-CM diluted 1:3 using SF-DMEM+Anti-Anti as diluent, then cultured 24h.

value: Pancreas

tag: cell line

value: Human PDAC

value: hAT-CM


title: Sample_Panc1_415

description: treated with hAT-CM from patient 5929-600415


title: Sample_Panc1_297

description: treated with hAT-CM from patient 5929-600297


title: PCF_AQ1_1

value: Lister 427

value: PCF


title: Sample_Panc1_277

description: treated with hAT-CM from patient 5929-600277


title: KO, replicated3, scRNAseq

city: Hangzhou

first: Xiaozhen

last: Zhang

state: Zhejiang

address: 79 QIngchun Road

department: Department of Hepatobiliary and Pancreatic Surgery

institute: the First Affiliated Hospital, School of Medicine, Zhejiang University

description: 10x Genomics

data_processing:
The final library pool was sequenced on the Illumina xx instrument using 150-base-pair paired-end reads.
Assembly: mm10
Supplementary files format and content: Tab-seperated valus files and matrix files

source_name: liver

extract_protocol:
For the quality check and counting of single cell suspension, the cell survival rate is generally above 80%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. The system is operated on the machine.
The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: liver

value: immune cells

value: Nek2 KO

value: Nek2 condition knock-out


title: defb_causp_m_het_1_1

description:
m_het_1_1_S1
Supplemental_Table_S6_7.xlsx


title: KO, replicated1, scRNAseq

description: 10x Genomics


title: defb_causp_m_het_1_2

description:
m_het_1_2_S2
Supplemental_Table_S6_7.xlsx


title: Sample_Panc1_363

description: treated with hAT-CM from patient 5929-600363


title: defb_causp_4_homo_miR_4_3

description:
4_homo_miR_4_4_S36
Supplemental_Table_S6_7.xlsx

value: Dgcr8fl/fl; Defb41-iCre cauda sperm

tag: rna microinjection

value: microRNA purified from cauda epididymosomes


title: WT, replicated2, scRNAseq

description: 10x Genomics

value: wildtype

value: ctrl


title: peripheral blood, colon polyps-r1 (RC604)

value: peripheral blood

value: M

value: colon polyps


title: Sample_Panc1_193

description: treated with hAT-CM from patient 600193


title: peripheral blood, colon polyps-r1 (RC601)

value: F


title: peripheral blood, colon polyps-r1 (RC600)


title: Sample_Mia_415

value: Pancreas


title: defb_causp_m_het_2_1

description:
m_het_2_1_S15
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: Morula

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: WT, replicated3, scRNAseq

description: 10x Genomics


title: peripheral blood, colon polyps-r1 (RC488)


title: peripheral blood, colon polyps-r1 (RC576)


title: defb_causp_4_homo_miR_4_2

description:
4_homo_miR_4_3_S30
Supplemental_Table_S6_7.xlsx


title: WT, replicated1, scRNAseq

description: 10x Genomics


title: Sample_Mia_363

value: Human PDAC

value: hAT-CM


title: Sample_Mia_319


title: defb_causp_4_homo_miR_3_6

description:
4_homo_miR_4_1_S18
Supplemental_Table_S6_7.xlsx


title: Sample_Mia_297


title: peripheral blood, colon polyps-r1 (RC579)


title: defb_causp_4_homo_miR_3_5

description:
4_homo_miR_3_6_S6
Supplemental_Table_S6_7.xlsx


title: C57 mice,diabetic ulcer,D3C1,Day14

city: Shanghai

first: Meijie

last: Yuan

state: --- Select One ---

address: 528 Zhangheng Road, Pudong New Area

institute: Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

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 fration: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: tab-delimited text file include TPM counts for each Sample

source_name: skin tissue

extract_protocol:
miRNA was harvested using mirVana miRNA Isolation Kit (Ambion),1ug of total miRNA was used for the construction of sequencing libraries.
miRNA libraries for samll RNA-seq were prepared using the Illumina HiSeq X Ten platform

value: skin tissue

tag: group

value: diabetic


title: C57 mice,diabetic ulcer,D3C2,Day14

tag: tissue


title: C57 mice,diabetic ulcer,D3C3,Day14


title: peripheral blood, colon polyps-r1 (RC427)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

tag: gender


title: peripheral blood, colon polyps-r1 (RC429)

tag: age


title: peripheral blood, colon polyps-r1 (RC458)

tag: cancer dx


title: defb_causp_4_homo_miR_3_4

description:
4_homo_miR_3_5_S33
Supplemental_Table_S6_7.xlsx

tag: developmental stage


title: peripheral blood, colon polyps-r1 (RC428)


title: Sample_Mia_277


title: peripheral blood, colon polyps-r1 (RC425)


title: C57 mice,normal ulcer, D3M3,Day14

value: normal


title: defb_causp_4_homo_miR_4_1

description:
4_homo_miR_4_2_S24
Supplemental_Table_S6_7.xlsx

tag: fvb/nj donor egg fertilized by

value: Dgcr8fl/fl; Defb41-iCre cauda sperm


title: defb_causp_4_homo_miR_3_3

description:
4_homo_miR_3_4_S32
Supplemental_Table_S6_7.xlsx

value: microRNA purified from cauda epididymosomes

tag: genome build


title: defb_causp_4_homo_miR_3_2

description:
4_homo_miR_3_3_S31
Supplemental_Table_S6_7.xlsx


title: Sample_Mia_193

description: treated with hAT-CM from patient 600193

tag: cell type


title: Sample_HPNE_415

value: human ductal (immortalized)


title: C57 mice,normal ulcer, D3M2,Day14


title: Sample_HPNE_363


title: peripheral blood, colon polyps-r1 (RC410)


title: defb_causp_4_homo_miR_3_1

description:
4_homo_miR_3_2_S30
Supplemental_Table_S6_7.xlsx


title: Sample_HPNE_319

description: treated with hAT-CM from patient 5929-600319


title: defb_causp_4_homo_miR_2_8

description:
4_homo_miR_2_8_S39
Supplemental_Table_S6_7.xlsx


title: GCB, WT, D13

city: Xihu District, Hangzhou

first: Xing

last: Chang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v.6.1.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: spleen

extract_protocol:
13 days after immunization, GCB cells from WT or Pcbp1 GCB KO mice were sorted and suspended in PBS with 0.4% FBS.
Library was performed according to manuscript's instructions ( single cell 3' v2 protocol, 10xgenomics). Briefly, GCB cells  were resuspended in the master mix and loaded with partitioning oil and gel beds into the chip to generate the gel bead-in-emulsion(GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane Dynabeads, ampllified by PCR and the apropriated size fragments were selected with SPRIselect regeant for subsequent library construction. During the liabrary consruction illunima R2 primer sequence, paired-end consructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: 100 μL of 1 mg/mL NP-KLH (Biosearch, N5060) and 100 μL of Album adjuvant (Thermo Scientific, 77161) were gently mixed upside down at room temperature for 30 min. 200 μL of emulsified NP-KLH was injected i.p into mice. Cells were collected on day 13 after immunization.

value: spleen

value: primary B cells

value: NP GCB

tag: genotype

value: WT

value: NPKLP immunization


title: GCB, KO, D13

value: KO

tag: treatment


title: C57 mice,normal ulcer, D3M1,Day14


title: Sample_HPNE_297

description: treated with hAT-CM from patient 5929-600297

value: Pancreas


title: defb_causp_4_homo_miR_2_6

description:
4_homo_miR_2_6_S27
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: Sample_HPNE_277

description: treated with hAT-CM from patient 5929-600277


title: defb_causp_4_homo_miR_2_5

description:
4_homo_miR_2_5_S21
Supplemental_Table_S6_7.xlsx


title: Sample_HPNE_193

description: treated with hAT-CM from patient 600193


title: defb_causp_4_homo_miR_2_4

description:
4_homo_miR_2_4_S24
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC405)

value: peripheral blood

value: M

value: colon polyps


title: Sample_Panc1_SF

description: serum free media treated cells

value: Human PDAC

value: SF


title: defb_causp_4_homo_miR_2_3

description:
4_homo_miR_2_3_S13
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC352)


title: Wild type P3 cochlear,rep3

city: Nanjing

first: Guoqiang

last: Wan

state: Jiangsu

address: Xuefu Road 12

department: Medical School

institute: Nanjing University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The sequences were processed and analyzed by Majorbio. Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were set < 0.05 to detect differential expressed ones.
Assembly: mm8
Supplementary files format and content: speadsheet files include RPKM values for each Sample

source_name: cochlear

extract_protocol:
Total RNA of cochleae from P3 wildtype and Pou4f3(Δ/+) mice was extracted using RNAiso plus kit (TaKaRa, Japan). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), NanoDrop (Thermo Fisher Scientific, USA) and 1% agarose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlear

value: wild type


title: Plscr5-/- P3 cochlear,rep3


title: Wild type P3 cochlear,rep2


title: Wild type P3 cochlear,rep1


title: peripheral blood, colon polyps-r1 (RC379p)


title: peripheral blood, colon polyps-r1 (RC3504)


title: peripheral blood, colon polyps-r1 (RC356)

value: F


title: defb_causp_4_homo_miR_2_2

description:
4_homo_miR_2_2_S43
Supplemental_Table_S6_7.xlsx

value: Dgcr8fl/fl; Defb41-iCre cauda sperm

value: microRNA purified from cauda epididymosomes


title: peripheral blood, colon polyps-r1 (RC394)


title: peripheral blood, colon polyps-r1 (RC344)


title: peripheral blood, colon polyps-r1 (RC347)


title: Plscr5-/- P3 cochlear,rep2


title: defb_causp_4_homo_miR_2_1

description:
4_homo_miR_2_1_S38
Supplemental_Table_S6_7.xlsx


title: Sample_Panc1.963_CAM

description: treated with hAT-CM from patient 35963

value: hAT-CM


title: Plscr5-/- P3 cochlear,rep1


title: Sample_Panc1.923_CAM_v2

description: treated with hAT-CM from patient 35923


title: peripheral blood, colon polyps-r1 (RC340)


title: defb_causp_4_homo_miR_1_6

description:
4_homo_miR_1_6_S42
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC334)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: Sample_Panc1.963_SF

description: serum free media treated cells (same time as cells treated from patient 35963 hAT-CM)


title: Sample_Mia_SF

description: treated with serum free media treated cells


title: Sample_Mia.963_SF

description: treated with serum free media treated cells (same time as cells treated from patient 35963 hAT-CM)


title: IR D5C

city: Wuhan

first: Yinzheng

last: Li

address: No. 1095, Jiefang Avenue, Wuhan, China. 430030

institute: Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology,

data_processing:
The original reads were demultiplexed and mapped to the reference genome using the 10× Genomics Cell Ranger. Unique molecule identifiers (UMIs) were counted for each gene and each cell barcode to construct a digital expression matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every genes and every cell

source_name: kidney

extract_protocol:
The left and right kidneys were transferred to new sterile culture dishes and minced. 5 mL of sterile PBS and the dissociation solution from the Multi Tissue dissociation kit (Miltenyi, 130-110-203) were added to the dish. The tissue and liquid in the dish were transferred to EP tube and placed on a 37°C shaking incubator for digestion. After 30 minutes, the digested tissue was filtered with 40μm cell strainer. The filtered cell digestion solution was collected into 15 mL centrifuge tube. After centrifugation, the supernatant was discarded, cell pellet was incubated with 1 ml of RBC lysis buffer on ice for 3 mins. The reaction was deactivated by adding sterile PBS. After centrifugation, cell counting was performed, and PBS was added to dilute the cell concentration to 10^6 cells/mL to obtain a single-cell suspension. The cell count and viability were analyzed using the Countess AutoCounter (Invitrogen, C10227).
The single-cell suspension, 10× barcoded gel beads, and oil were added to the wells of a single-cell sequencing chip according to the instructions, forming a droplet containing a single cell. Single-cell 5' sequence-related reagents were added to the system following a standardized process. Reverse transcription was then performed to generate cDNA, followed by PCR amplification for subsequent sequencing.

value: kidney

value: IR D5


title: IR D14

value: IR D14


title: IR D28

value: IR D28


title: defb_causp_4_homo_miR_1_5

description:
4_homo_miR_1_5_S37
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC346)


title: defb_causp_4_homo_miR_1_2

description:
4_homo_miR_1_2_S12
Supplemental_Table_S6_7.xlsx


title: Sample_Mia.963_CAM

description: treated with hAT-CM from patient 35963

value: Pancreas


title: peripheral blood, colon polyps-r1 (RC3113)


title: Sample_Mia.923_CAM_v2

description: treated with hAT-CM from patient 35923


title: peripheral blood, colon polyps-r1 (RC316)


title: IR D5A


title: IR D5B


title: defb_causp_4_homo_miR_1_8

description:
4_homo_miR_1_8_S8
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: peripheral blood, colon polyps-r1 (RC283)

value: peripheral blood


title: peripheral blood, colon polyps-r1 (RC2546)


title: defb_causp_4_homo_miR_1_1

description:
4_homo_miR_1_1_S11
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC2697)


title: defb_causp_4_homo_con_4_4

description:
4_homo_con_4_4_S12
Supplemental_Table_S6_7.xlsx

value: Control RNA


title: defb_causp_4_homo_con_4_3

description:
4_homo_con_4_3_S17
Supplemental_Table_S6_7.xlsx


title: Sample_HPNE.963_SF

value: human ductal (immortalized)


title: Sample_HPNEG12D_SF

description: serum free media treated cells


title: Sample_HPNE.963_CAM_v2

description: treated with hAT-CM from patient 35963


title: IR D1

value: IR D1


title: IR H12

value: IR H12


title: defb_causp_4_homo_con_4_2

description:
4_homo_con_4_2_S37
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC249)

value: M

value: colon polyps


title: IR H4

value: IR H4


title: defb_causp_4_homo_con_4_1

description:
4_homo_con_4_1_S36
Supplemental_Table_S6_7.xlsx

value: Dgcr8fl/fl; Defb41-iCre cauda sperm


title: Sample_HPNE.923_CAM_v2

description: treated with hAT-CM from patient 35923


title: ShamB

value: Sham


title: ShamA


title: defb_causp_4_homo_con_3_6

description:
4_homo_con_3_6_S5
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_homo_con_3_4

description:
4_homo_con_3_4_S40
Supplemental_Table_S6_7.xlsx


title: Mitosis HeLa, GFP-FOXA1, WT-group2, CUT&Tag (K8)

city: hefei

first: 张

last: 婷

state: Select an option…

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

institute: 中国科学技术大学

description:
Illumina NovaSeq PE150
HeLa-K8-GFP-FOXA1-WT-Mitosis-2

library_source: genomic

data_processing:
*library strategy: CUT&Tag
Then libraries with different indices were multiplexed and loaded on an Illumina Novaseq instrument according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150 paired-end (PE) configuration, and image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument. In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format  were processed by Cutadapt to be high-quality clean data. The clean data then are aligned to the reference genome via software Bowtie2. Use MACS to analyze peaks quality control, peaks calling and peaks annotation. To find the common and unique peaks of several groups, HOMER(V2) toolkit is used to treat the peaks with 200bp overlapping peaks as common and vice versa.
Assembly: GRCh38.109
Supplementary files format and content: The processed data consisted of a bw file for each sample and a table of the corresponding peaks

molecule: genomic DNA

source_name: Stably expressing GFP-FOXA1 HeLa cell

growth_protocol: HeLa cells were maintained in DMEM (Gibco) with 10% fetal bovine serum (HyClone) and 100 units/ml penicillin (Gibco) plus 100 μg/ml streptomycin (Gibco)

extract_protocol:
See Vazyme TD904
Next-generation sequencing library preparations were constructed following the manufacturer’s protocol (Vazyme TD202)

treatment_protocol: thymidine 2mM 16 h to block the cell in G1/S (interphase)；Nocodazole 100 ng/ml 16 h to block the cell in G2/M (mitosis)

value: Stably expressing GFP-FOXA1 HeLa cell


title: Mitosis HeLa, GFP-FOXA1, WT-group1, CUT&Tag (K7)

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

description:
Illumina NovaSeq PE150
HeLa-K7-GFP-FOXA1-WT-Mitosis


title: CD6rest

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

description: OE-F

data_processing:
Basecalls performed using CASAVA version 1.4
Each dataset was filtered for average base quality score (>20)
Filtered datasets were aligned to a reference genome using Bismark v0.7.8 (parameters-X 10000 --non_bs_mm -n 2 -l 50 -e 70 --chunkmbs 1024)41, using Bowtie v0.12.842 as the underlying alignment tool. The reference genome index contained the genome sequence of enterobacteria phage λ (NC_001416.1) in addition to all chromosomes of the mm9 assembly. Mappings for all datasets generated from the same library were merged, and duplicates removed via the Bismark deduplication tool (deduplicate_bismark_alignment_output.pl).
Mapped reads were then separated by genome (mm9 or phage λ) and by source strand (plus or minus)
The first four and last one base of each read2 in all read pairs was clipped due to positional methylation bias, and any redundant mapped bases due to overlapping mates from the same read pair were trimmed to avoid bias in quantification of methylation status. Finally, SAM alignments for multiple libraries from the same animal were merged. Read pairs mapped to phage λ were used as a QC assessment to confirm that the observed bisulfite conversion rate was >99%. Read pairs mapped to the mm10 reference genome were used for downstream analysis
Assembly: GRCm38 - mm10
Supplementary files format and content: txt file includes CT frequency values for each sample
Supplementary files format and content: txt file includes CT frequency values for each sample

source_name: medial frontal cortex

extract_protocol:
Genomic DNA was extracted from mouse using DNeasy Blood & Tissue Kit
Genomic DNA was processed with the Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.

value: medial frontal cortex

tag: Sex

value: Female


title: peripheral blood, colon polyps-r1 (RC230)


title: CD16rest

description: OE-F

tag: strain


title: peripheral blood, colon polyps-r1 (RC2306)

value: F


title: defb_causp_4_homo_con_3_3

description:
4_homo_con_3_3_S34
Supplemental_Table_S6_7.xlsx


title: Mitosis HeLa, GFP-FOXA1, S221A-group2, CUT&Tag (K6)

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

description:
Illumina NovaSeq PE150
HeLa-K6-GFP-FOXA1-S221A-Mitosis-2

source_name: Stably expressing GFP-FOXA1-S221A HeLa cell


title: Mitosis HeLa, GFP-FOXA1, S221A-group1, CUT&Tag (K5)

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

description:
Illumina NovaSeq PE150
HeLa-K5-GFP-FOXA1-S221A-Mitosis

value: Stably expressing GFP-FOXA1-S221A HeLa cell


title: peripheral blood, colon polyps-r1 (RC2141)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: defb_causp_4_homo_con_3_2

description:
4_homo_con_3_2_S28
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_homo_con_2_8

description:
4_homo_con_2_8_S21
Supplemental_Table_S6_7.xlsx


title: D-1

description: OE-F


title: Interphase HeLa, GFP-FOXA1, WT-group2, CUT&Tag (K4)

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

description:
Illumina NovaSeq PE150
HeLa-K4-GFP-FOXA1-WT-interphase-2


title: CF1rest

description: OE-M

value: Male


title: CD5rest

description: OE-M


title: Interphase HeLa, GFP-FOXA1, WT-group1, CUT&Tag (K3)

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

description:
Illumina NovaSeq PE150
HeLa-K3-GFP-FOXA1-WT-interphase


title: defb_causp_4_homo_con_2_7

description:
4_homo_con_2_7_S9
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: CC2rest

description: OE-M


title: peripheral blood, colon polyps-r1 (RC2011)

value: peripheral blood


title: peripheral blood, colon polyps-r1 (RC201)


title: peripheral blood, colon polyps-r1 (RC2016)


title: peripheral blood, colon polyps-r1 (RC187)


title: peripheral blood, colon polyps-r1 (RC2119)


title: peripheral blood, colon polyps-r1 (RC186)


title: KO, replicated2, scRNAseq

description: 10x Genomics

value: liver

value: immune cells

value: Nek2 KO

value: Nek2 condition knock-out


title: defb_causp_4_homo_con_2_5

description:
4_homo_con_2_5_S23
Supplemental_Table_S6_7.xlsx

value: Control RNA


title: B-4

description: CON-F


title: B-5

description: CON-F


title: B-3

description: CON-F


title: defb_causp_4_homo_con_2_3

description:
4_homo_con_2_3_S32
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_homo_con_2_4

description:
4_homo_con_2_4_S22
Supplemental_Table_S6_7.xlsx


title: RNA-seq_PB2_KO_AML2

city: Houston

first: Anand

last: Singh

address: 1901 East Road

institute: MD Anderson Cancer Center

data_processing:
The quality of raw reads was evaluated using FastQC. The raw reads were aligned to the Homo sapiens genome (hg19) using STAR. Differential expression analysis was performed using DESeq2. Genes were normalized and analyzed for differential expression using the DESeq2. Genes with an absolute log2 fold-change greater than log2(1.5) and padj < 0.05 were identified as differentially expressed.
Assembly: hg19
Supplementary files format and content: genes.results

source_name: blood

extract_protocol:
Illumina Compatible lowinputmRNA libraries were prepared using the Smart-Seq V4 Ultra LowInputRNA kit (Takara Bio, USA) and KAPA HyperPlus Library Preparation kit (Roche). Briefly, full length, double stranded cDNA was generated from 10ng of total RNA using Takara’s SMART (SwitchingMechanismat 5’ End ofRNATemplate) technology. The ds cDNA was amplified by 5 cycles of LD-PCR, then purified using Ampure Beads (Agencourt). Following bead elution, the cDNA was evaluatedforsize distribution and quantity using 4200 TapeStation High Sensitivity D1000 ScreenTape-Agilent Technologiesand the Qubit dsDNA HS Assay Kits(ThermoFisher) respectively.
The cDNA was enzymatically fragmented, and 10ng of the fragmented cDNA was used to generate Illumina compatible libraries using the KAPA HyperPlus Library Preparation kit.  The KAPA libraries were purified and enriched with 8 cycles of PCR to create the final cDNA library. The libraries were assessed for size distribution using the Agilent Tapestation and quantified using the Qubit™ dsDNA HS Assay (ThermoFisher), then equimolar quantities of 33 libraries were combined to create the final library pool. The pooled library was quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) and assessed for size distribution using the TapeStation 4200 (Agilent Technologies), then sequenced on the Illumina NovaSeq6000 SP flow cell using the 100nt paired end run format.

value: blood

value: NK Cells

value: primary cells


title: CF2rest

description: CON-M


title: peripheral blood, colon polyps-r1 (RC170)

value: M

value: colon polyps


title: RNA-seq_PB1_KO_AML2


title: RNA-seq_PB2_CAS9_AML1


title: RNA-seq_PB2_CAS9_AML2


title: defb_causp_4_homo_con_2_2

description:
4_homo_con_2_2_S20
Supplemental_Table_S6_7.xlsx

value: Dgcr8fl/fl; Defb41-iCre cauda sperm


title: defb_causp_4_homo_con_1_8

description:
4_homo_con_1_8_S27
Supplemental_Table_S6_7.xlsx


title: Interphase HeLa, GFP, control, CUT&Tag (C1)

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

description:
Illumina NovaSeq PE150
HeLa-C1-GFP

source_name: Stably expressing GFP HeLa cell

value: Stably expressing GFP HeLa cell


title: RNA-seq_PB1_KO_AML1


title: defb_causp_4_homo_con_2_6

description:
4_homo_con_2_6_S3
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC1608)

source_name: peripheral blood

value: F


title: CC3rest

description: CON-M

value: medial frontal cortex


title: RNA-seq_PB1_CAS9_TRANSWELL_AML1


title: defb_causp_4_homo_con_1_7

description:
4_homo_con_1_7_S9
Supplemental_Table_S6_7.xlsx

source_name: preimplantation embryo


title: CC1rest

description: CON-M

value: Male


title: peripheral blood, colon polyps-r1 (RC1561)


title: defb_causp_4_homo_con_1_6

description:
4_homo_con_1_6_S8
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: peripheral blood, colon polyps-r1 (RC153)

value: peripheral blood


title: peripheral blood, colon polyps-r1 (RC1541)


title: peripheral blood, colon polyps-r1 (RC1479)


title: TNF_3, stimulated MSCs with TNF-α

city: Okayama

first: Kentaro

last: Akiyama

address: 2-5-1 Shikata Cho

department: Department of Oral Rehabilitation and Regenerative Medicine

country: Japan

institute: Okayama University

data_processing:
Illumina NovaSeq 6000 Sequencer (Illumina) was used for sequencing.
After quality trimming using Trim Galore, the STAR aligner was used to map the reads according to reference genome (GRCm39, Ensembl release 107).
StringTie and SQANTI3 were used to generate and annotate nova transcripts, respectively.
Salmon software was used to re-quantify all samples at the transcript level, and isoformSwitchAnalyzeR based on Salmon's mapping results, was used to perform additional quality filtering.
The median read number of all gene transcripts was used to estimate the gene expression levels.
Assembly: GRCm39 Ensembl release 105
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: mesenchymal stem cells

growth_protocol: Bone marrow-derived MSCs from C57BL/6J mice were maintained in α-MEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using RNeasy Plus Micro Kit (QIAGEN) and treated with Dnase (Life Technologies) according to conventional protocol. RNA concentration and quality were measured using a Tapestation 2200 (Agilent Technologies).
RNA libraries for RNA-seq  were prepared using SMART-Seq Stranded Kit (Takara Bio USA Inc.) following manufacturer's protocol.

treatment_protocol: MSCs were stimulated with 10 ng/mL TNF-α for 24 hours and unstimulated MSCs as controls.

value: mesenchymal stem cells

value: WT

value: TNF-alpha treatment

tag: time


title: defb_causp_4_homo_con_1_5

description:
4_homo_con_1_5_S31
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_homo_con_1_4

description:
4_homo_con_1_4_S15
Supplemental_Table_S6_7.xlsx


title: RNA-seq_PB1_CAS9_AML2_TRANSWELL


title: peripheral blood, colon polyps-r1 (RC128)


title: Cont_3, unstimulated MSCs

value: No treatment


title: RNA-seq_CONTROL_PB2_KO


title: TNF_2, stimulated MSCs with TNF-α


title: RNA-seq_CONTROL_PB2_CAS9


title: peripheral blood, colon polyps-r1 (RC1288)


title: RNA-seq_CONTROL_PB1_KO


title: RNA-seq_PB1_Cas9_AML_transwell


title: peripheral blood, colon polyps-r1 (RC1473)


title: defb_causp_4_homo_con_1_2

description:
4_homo_con_1_2_S15
Supplemental_Table_S6_7.xlsx

value: Control RNA


title: defb_causp_4_homo_con_1_3

description:
4_homo_con_1_3_S19
Supplemental_Table_S6_7.xlsx


title: Cont_2, unstimulated MSCs


title: defb_causp_4_homo_con_1_1

description:
4_homo_con_1_1_S7
Supplemental_Table_S6_7.xlsx


title: Cont_1, unstimulated MSCs


title: CT-PB2-KO

data_processing:
The paired-end ATAC-seq reads were trimmed for illumine adapter with atactk and aligned to  reference genome with Bowtie2. All unmapped reads, non-uniquely mapped reads, PCR duplicates and mitochondrial chromosome were removed, along with down sampling of sequences with Bowtie2 and SAMBLASTER. Aligned reads were normalized offers normalization by Reads Per Kilobase per Million mapped reads (RPKM) scaling factor by using bamCoverage of deepTools. ATAC-seq peaks were called using MACS2.
Assembly: hg19
Supplementary files format and content: narrowPeak

source_name: Blood

extract_protocol:
50,000 nuclei isolated from NK cells from different experimental set ups were subjected to tagmentation using Tagment DNA enzyme (Illumina) followed by library preparation and DNA cleanup using SPRISelect beads (Beckman Coulter)
ATAC-seq library preparation was performed at the MDACC Epigenomics Profiling Core using NEBNext High-Fidelity 2x PCR Master Mix and iIllumina Primers and tagmented DNA.

value: Blood

value: NK Cell


title: RNA-seq_CONTROL_PB1_CAS9

value: blood

value: NK Cells

value: primary cells


title: TNF_1, stimulated MSCs with TNF-α


title: Neurod1-Cre, caecum, scRNA-seq

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: 10x Genomics

data_processing:
Quality controls, read alignment, and raw count quantification for each cell were generated using the CellRanger pipeline (v6.1.2, 10x Genomics).
Assembly: mm39 genome, downloaded from the UCSC genome browser.
Supplementary files format and content: Count matrices, exported by CellRanger, are H5 format.
Supplementary files format and content: Seurat objects are in RDS format, for import into R, including normalised data, and tSNE maps.
Supplementary files format and content: Cluster markers are in CSV format, consisting of a list of differentially expressed genes per region per cluster.

source_name: Caecum

extract_protocol:
Adult NeuroD1-Cre x EYFP mice were culled by cervical dislocation, GI tracts were removed and digested to single cell suspension, and sorted for EYFP fluorescence using an Influx Cell Sorter (BD Biosciences) at the Cambridge Institute of Medical Research (CIMR) Flow Cytometry Core Facility. DAPI and DRAQ5 staining, side scatter, forward scatter and pulse width gates were used to remove debris and cell clusters.
cDNA library preparations were performed using the Chromium system (10X Genomics) by the Genomics Core Facilities at the Cancer Research UK (CRUK) Cambridge Institute (for the USI, LSI and LI) and the Wellcome-MRC Cambridge Stem Cell Institute (for the stomach and caecum).

value: Caecum

value: EECs

value: NeuroD1-Cre x EYFP

value: female


title: CT-PB2-CAS9


title: peripheral blood, colon polyps-r1 (RC1279)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

extract_protocol: Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.

value: M

value: colon polyps


title: peripheral blood, colon polyps-r1 (RC124)

value: peripheral blood


title: Neurod1-Cre, lower small intestine, scRNA-seq

description: 10x Genomics

source_name: Lower small intestine

value: Lower small intestine


title: Neurod1-Cre, upper small intestine, scRNA-seq

description: 10x Genomics

source_name: Upper small intestine

value: Upper small intestine


title: peripheral blood, colon polyps-r1 (RC1209)


title: defb_causp_4_het_4_4

description:
4_het_4_4_S35
Supplemental_Table_S6_7.xlsx

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

extract_protocol:
RNA was isolated using RNA-Clean XP beads
Illumina Nextera XT Kit

value: preimplantation embryo

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: peripheral blood, colon polyps-r1 (RC1240)

value: F


title: peripheral blood, colon polyps-r1 (RC1207)


title: CT-PB1-KO

value: Blood


title: CT-PB1-CAS9

value: NK Cell


title: D-3 [miRNA]

description:
OE-F
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls

data_processing:
Bcl2fastq (v2.17.1.14) software was used for base-calling
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
All transcripts as the result of Cuffmerge, were filtered by known non-lincRNA annotation, non- lincRNA characters, ORFs and protein-coding potential methods. Known non-lincRNA includes known protein-coding RNA, miRNA, tRNA, snoRNA, rRNA and pseudogenes. There are three characters of non-lincRNA, such as transcripts of non-lincRNA contain more than one exon; their length must be longer than 200bp; and the coverage of each transcript must be more than 3. ORFs were predicted by software HMMER (v3.1b1). CPC (Coding Potential Calculator) was used to do protein-coding potential prediction. CNCI (Coding-Non-Coding Index), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. Transcriptional regulation by lncRNAs could work either in cis or in trans, and could negatively or positively control pc gene expression. lncRNAs work in cis when their effects are restricted to the chromosome from which they are transcribed, and work in trans when they affect genes on other chromosomes. The cis regulation by lncRNAs can be predicted by software Bedtools (v2.17.0). And regulation in trans was analyzed via Pearson correlation coefficient.
Assembly: ENSEMBLE GRCm38.100
Supplementary files format and content: xls file includes FPKM values for each sample

extract_protocol:
The total RNA of each sample was extracted from the medial frontal cortex of mouse brain by using TRIzol reagent (Life Technologies, USA)/RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s protocol. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The rRNA was depleted from total RNA using rRNA removal Kit. The ribosomal depleted RNA was then fragmented and reverse-transcribed. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix (include dACG-TP/dUTP). The purified double-stranded cDNA by beads 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 beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. The dUTP-marked second strand was digested with Uracil-Specific Excision Reagent enzyme. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P5/P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA,USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA) or a MGI2000 instrument according to manufacturer’s instructions (MGI, Shenzhen, China) . Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline- 1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.

value: medial frontal cortex

tag: development stage

value: Female


title: AML2-PB2-KO

tag: cell line

value: primary cells


title: peripheral blood, colon polyps-r1 (RC117p)


title: defb_causp_4_het_4_1

description:
4_het_4_1_S38
Supplemental_Table_S6_7.xlsx


title: AML2-PB1-KO


title: AML2-PB2-CAS9


title: defb_causp_4_het_4_2

description:
4_het_4_2_S23
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_het_4_8

description:
4_het_4_8_S35
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_het_4_5

description:
4_het_4_5_S41
Supplemental_Table_S6_7.xlsx


title: D-1 [miRNA]


title: defb_causp_4_het_4_7

description:
4_het_4_7_S34
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_het_3_8

description:
4_het_3_8_S16
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC110)


title: AML2-PB1-CAS9-TRANSWELL


title: Neurod1-Cre, stomach, scRNA-seq

description: 10x Genomics

source_name: Stomach

value: Stomach

value: male


title: defb_causp_4_het_3_7

description:
4_het_3_7_S28
Supplemental_Table_S6_7.xlsx


title: C-3 [miRNA]

description:
OE-M
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls

value: Male


title: defb_causp_4_het_3_6

description:
4_het_3_6_S10
Supplemental_Table_S6_7.xlsx


title: AML-PB2KO


title: peripheral blood, colon polyps-r1 (RC1087B)


title: peripheral blood, colon polyps-r1 (RC1111)


title: peripheral blood, colon polyps-r1 (RC101)


title: D-2 [miRNA]


title: peripheral blood, colon polyps-r1 (RC1048)


title: defb_causp_4_het_3_5

description:
4_het_3_5_S26
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC0966)


title: C-1 [miRNA]


title: C-2 [miRNA]


title: peripheral blood, colon polyps-r1 (RC094)


title: AML-PB2-CAS9


title: B-3 [miRNA]

description:
CON-F
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls


title: defb_causp_4_het_3_4

description:
4_het_3_4_S25
Supplemental_Table_S6_7.xlsx


title: AML-PB2-CAS9-TRANSWELL


title: defb_causp_4_het_3_3

description:
4_het_3_3_S10
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_het_3_2

description:
4_het_3_2_S4
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC0964)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: AML-PB1-CAS9


title: AML-PB1-KO


title: defb_causp_4_het_3_1

description:
4_het_3_1_S44
Supplemental_Table_S6_7.xlsx


title: B-1 [miRNA]


title: AML-PB1-CAS9-TRANSWELL


title: A-3 [miRNA]

description:
CON-M
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls


title: A-2 [miRNA]


title: B-2 [miRNA]


title: defb_causp_4_het_2_8

description:
4_het_2_8_S19
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_het_2_7

description:
4_het_2_7_S18
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC0920)


title: FICZ_IL4_2

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of sequencing data was assessed using FastQC
Reads were aligned to the genome using BWA-Mem
Peak calling was performed with MACS2
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Blood monocytes from 3 individual donors were stimulated for 20 min in the presence of 5 ng/mL of IL4 in complete medium, in the presence of 8 microM SR1 (Cayman chemicals) or 60nM FICZ (Enzo Life Sciences) . Chromatin immunoprecipitation was performed from 80 millions monocytes as starting material, using the ChIP-IT High Sensitivity kit (Active Motif) following manufacturer’s instructions. Chromatin was immunoprecipitated using an antibody against STAT6 (clone 7D3, ThermoFisher)..
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIPSeq Library Prep Kit (Illumina). 1 ng of DNA was used for each sample.
Sequencing was performed in 1 sequencing unit of NovaSeq 6000 (Illumina) (100-nt593 length reads, paired end).

value: blood

value: monocyte

tag: antibody


title: A-1 [miRNA]


title: peripheral blood, colon polyps-r1 (RC090)

city: Richmond

first: Adam

last: Dempsey

institute: StageZero Life Sciences

value: M

value: colon polyps


title: peripheral blood, colon polyps-r1 (RC089)

value: peripheral blood


title: peripheral blood, colon polyps-r1 (RC0912)


title: peripheral blood, colon polyps-r1 (RC0922)


title: FICZ_IL4_1


title: WTIL4_7

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Assembly: mm10
Supplementary files format and content: Count matrix (raw counts) in csv format.

source_name: bone marrow

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample.
Sequencing was performed in 3 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end) with an average depth of 40 millions of clusters per sample.

treatment_protocol: Bone marrows were flushed out from legs. Monocytes were purified with EasySep mouse monocyte isolation kit (Stemcell) according to manufacturer’s recommendations. Cells were 90-95% pure as verified by flow cytometry. Mouse monocytes were cultured in the presence or absence of 20 ng/mL of mouse IL-4.

value: bone marrow


title: defb_causp_4_het_2_6

city: Philadelphia

first: Natalie

last: Trigg

institute: Children's Hospital of Philadelphia

description:
4_het_2_6_S17
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: defb_causp_4_het_2_5

description:
4_het_2_5_S16
Supplemental_Table_S6_7.xlsx

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: SR1_IL4_3


title: defb_causp_4_het_2_4

description:
4_het_2_4_S25
Supplemental_Table_S6_7.xlsx


title: KOIL4_6


title: defb_causp_4_het_2_3

description:
4_het_2_3_S14
Supplemental_Table_S6_7.xlsx


title: SR1_IL4_1


title: peripheral blood, colon polyps-r1 (RC077)


title: SR1_IL4_2


title: KOIL4_5


title: FICZ_IL4_3

value: v


title: defb_causp_4_het_2_2

description:
4_het_2_2_S20
Supplemental_Table_S6_7.xlsx


title: input_3


title: peripheral blood, colon polyps-r1 (RC0879)


title: input_2


title: WTIL4_3


title: WTIL4_2


title: peripheral blood, colon polyps-r1 (RC070)


title: defb_causp_4_het_1_8

description:
4_het_1_8_S7
Supplemental_Table_S6_7.xlsx


title: defb_causp_4_het_2_1

description:
4_het_2_1_S14
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colon polyps-r1 (RC0765)


title: WTIL4_1


title: Wtmedium_7

value: medium


title: defb_causp_4_het_1_7

description:
4_het_1_7_S6
Supplemental_Table_S6_7.xlsx


title: KOIL4_4


title: ARP1 cells, c-Maf-IDR, IP

city: nanjing

first: wang

last: ze

address: qixia

institute: Nanjing University Of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1).
MACS2(version 2.2.7.1) was used to call peaks. IGV software was used to visualize called peaks from ChIP-seq samples. Called peaks were then annotated using R package ChIPseeker.
HOMER (http://homer.ucsd.edu/homer/download.html, v4.11.1) were used to find de novo and known motif.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Peripheral blood

extract_protocol:
1. Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. 2. Extract chromatin from cross-linked cells by adding Lysis Buffer. 3. Sonicate chromatin DNA to fragments ranging from 100 to 500 bp. 4. Immunoprecipitate chromatin DNA and antibody-associated beads by incubating them 5. Wash Dynabeads for eluting immunoprecipitated protein-DNA complexes by optimal method.
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X)和 End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min. And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads.  Qubit was used for library quantification and High-sensitivity DNA chip was used for test of library insert size.

value: Peripheral blood

value: Tumor cell

tag: chip antibody

value: FLAG


title: ARP1 cells, c-Maf, IP

tag: tissue


title: peripheral blood, colon polyps-r1 (RC074)

address: 8751 Park Central Drive, Suite 200

tag: gender


title: Komedium_6


title: defb_causp_4_het_1_5

address: 421 Curie Blvd

description:
4_het_1_5_S4
Supplemental_Table_S6_7.xlsx


title: Komedium_5


title: ARP1 cells, Ev, IP


title: input_1


title: ARP1 cells, c-Maf, Input


title: defb_causp_4_het_1_4

description:
4_het_1_4_S3
Supplemental_Table_S6_7.xlsx


title: Komedium_4


title: peripheral blood, colon polyps-r1 (RC0639)

tag: age


title: ARP1 cells, c-Maf-IDR, Input


title: peripheral blood, colon polyps-r1 (RC0660)

tag: cancer dx


title: defb_causp_4_het_1_6

description:
4_het_1_6_S5
Supplemental_Table_S6_7.xlsx

tag: developmental stage


title: Wtmedium_3


title: peripheral blood, colon polyps-r1 (RC0700)


title: ARP1 cells, Ev, Input


title: peripheral blood, colon polyps-r1 (RC058)


title: Wtmedium_2


title: Wtmedium_1


title: peripheral blood, colon polyps-r1 (RC056)

value: F


title: defb_causp_4_het_1_1

description:
4_het_1_1_S1
Supplemental_Table_S6_7.xlsx

tag: fvb/nj donor egg fertilized by


title: ovarian cancer P0996

city: Kyoto

first: Shiro

last: Takamatsu

address: 54 Shogoin Kawahara, Sakyo, Kyoto

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

data_processing:
Raw fastq files were trimmed using Trim-Galore, then mapped to the human reference genome (GRCh38) with the gene annotation of Ensemble GRCh38.v99 using STAR (v2.7.8a). Subsequently, gene expression levels were normalised as TPM or FPKM values using RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited text file includes gene TPM values for each sample
Supplementary files format and content: tab-delimited text file includes gene FPKM values for each sample

source_name: primary tumor

extract_protocol:
As per manufacturer protocol (SMART-Seq@Stranded Kit User Manual (022819), SMART-Seq@Stranded Kit, SMART-Seq@RNA Unique Dual Index Kit)
The cDNA was synthesized from the extracted total RNA using random primers, and a specific sequence was assigned to the end of the 1st strand cDNA by the SMART (Switching Mechanism At 5' End of RNA Template) method. The specific sequence was then amplified by PCR using primers with indexes having different tag sequences for each sample. The PCR product was purified by the magnetic bead method using AMPure XP (Beckman Coulter), and the ribosomal cDNA was cleaved using scZapR and scR-Probe. Finally, the uncut cDNA was PCR amplified using primers that recognize the adaptor, and a sequencing library was generated.
The quality of the generated sequence library was measured using an Agilent 2100 BioAnalyzer. The libraries were sequenced on Illumina NovaSeq6000. Depths of 180–350 million paired-end 150 bp reads were generated for each sample.

tag: disease state

value: ovarian cancer

value: primary tumor

tag: histology cpr

value: HGSC

tag: histology iti

value: Serous carcinoma

tag: assigned cluster


title: peripheral blood, colon polyps-r1 (RC060)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: peripheral blood, colon polyps-r1 (RC0637)


title: peripheral blood, colon polyps-r1 (RC062)


title: Muscle, myoblast, Rep7, siSirt1

city: Jena

first: Ellen

last: Spaeth

state: Thuringia

address: Beutenbergstraße 11

country: Germany

institute: FLI - Leibniz Institute on Aging

description:
150 bp sequencing
raw_counts_siCtrl-vs-siSirt1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siSirt1.csv
TPM_values_siLmod1-vs-siSirt1.csv
7_siSirt1

data_processing:
Read counts and normalization was done using DeSeq2 benchwork
Assembly: mm10
Supplementary files format and content: Comma-separated valuesfile includes raw counts for each Sample
Supplementary files format and content: Comma-separated valuesfile includes normalized counts for each Sample
Supplementary files format and content: Comma-separated valuesfile includes TPM values for each Sample

source_name: Muscle

growth_protocol: Primary myoblasts pre-treated with siRNA using siRNAiMax (ThermoFisher)

extract_protocol:
Total RNA was extracted using TriFast (Peqlab) according to the manufacturer's instructions
PolyA library preperation was done using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to manufacturer's protocol

value: Muscle

tag: cell type

value: primary myoblasts

tag: genotype

value: WT

tag: treatment


title: stra8_homo_cautis_4

description:
stra8_homo_cautis_4_S14
Supplemental_Table_S4_5.xlsx

source_name: cauda epididymis tissue

extract_protocol:
Total RNA was extracted from tissues
Illumina Stranded mRNA Kit

value: cauda epididymis tissue

value: Dgcr8fl/fl; Stra8-iCre

tag: genome build


title: ovarian cancer P0991


title: stra8_homo_cautis_3

description:
stra8_homo_cautis_3_S13
Supplemental_Table_S4_5.xlsx


title: Muscle, myoblast, Rep4, siSirt1

description:
150 bp sequencing
raw_counts_siCtrl-vs-siSirt1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siSirt1.csv
TPM_values_siLmod1-vs-siSirt1.csv
4_siSirt1

tag: strain


title: defb_causp_4_het_1_3

description:
4_het_1_3_S2
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: ovarian cancer P0978


title: defb_causp_4_het_1_2

description:
4_het_1_2_S1
Supplemental_Table_S6_7.xlsx

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: stra8_homo_cautis_2

description:
stra8_homo_cautis_2_S12
Supplemental_Table_S4_5.xlsx


title: Muscle, myoblast, Rep3, siSirt1

description:
150 bp sequencing
raw_counts_siCtrl-vs-siSirt1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siSirt1.csv
TPM_values_siLmod1-vs-siSirt1.csv
3_siSirt1


title: ovarian cancer P0973


title: stra8_homo_cautis_1

description:
stra8_homo_cautis_1_S11
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colon polyps-r1 (RC0493)

value: peripheral blood

value: M

value: colon polyps


title: peripheral blood, colon polyps-r1 (RC0498)


title: ovarian cancer P0970

value: Other


title: peripheral blood, colon polyps-r1 (RC055)


title: peripheral blood, colon polyps-r1 (RC0532)


title: peripheral blood, colon polyps-r1 (RC0482)


title: stra8_homo_captis_3

description:
stra8_homo_captis_3_S6
Supplemental_Table_S4_5.xlsx

source_name: caput epididymal tissue

value: caput epididymal tissue


title: stra8_homo_captis_2

description:
stra8_homo_captis_2_S5
Supplemental_Table_S4_5.xlsx


title: Muscle, myoblast, Rep1, siSirt1

description:
150 bp sequencing
raw_counts_siCtrl-vs-siSirt1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siSirt1.csv
TPM_values_siLmod1-vs-siSirt1.csv
1_siSirt1


title: ovarian cancer P0966


title: Muscle, myoblast, Rep7, siLmod1

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siLmod1-vs-siSirt1.csv
7_siLmod1


title: ovarian cancer P0968


title: stra8_homo_captis_1

description:
stra8_homo_captis_1_S4
Supplemental_Table_S4_5.xlsx


title: stra8_het_cautis_4

description:
stra8_het_cautis_4_S10
Supplemental_Table_S4_5.xlsx

value: Dgcr8+/fl; Stra8-iCre


title: Muscle, myoblast, Rep2, siSirt1

description:
150 bp sequencing
raw_counts_siCtrl-vs-siSirt1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siSirt1.csv
TPM_values_siLmod1-vs-siSirt1.csv
2_siSirt1


title: Muscle, myoblast, Rep3, siLmod1

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siLmod1-vs-siSirt1.csv
3_siLmod1


title: ovarian cancer P0956

value: ovarian cancer

value: Endometrioid carcinoma


title: Muscle, myoblast, Rep4, siLmod1

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siLmod1-vs-siSirt1.csv
4_siLmod1


title: stra8_het_cautis_3

description:
stra8_het_cautis_3_S9
Supplemental_Table_S4_5.xlsx


title: Muscle, myoblast, Rep2, siLmod1

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siLmod1-vs-siSirt1.csv
2_siLmod1


title: ovarian cancer P0993

value: primary tumor

value: HGSC


title: peripheral blood, colon polyps-r1 (RC047)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: ovarian cancer P0954

value: Serous carcinoma


title: stra8_het_cautis_2

description:
stra8_het_cautis_2_S8
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colon polyps-r1 (RC0490)


title: Muscle, myoblast, Rep1, siLmod1

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siLmod1-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siLmod1-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siLmod1-vs-siSirt1.csv
1_siLmod1

value: Muscle

value: primary myoblasts


title: ovarian cancer P0952


title: stra8_het_cautis_1

description:
stra8_het_cautis_1_S7
Supplemental_Table_S4_5.xlsx

value: cauda epididymis tissue


title: peripheral blood, colon polyps-r1 (RC0454)


title: peripheral blood, colon polyps-r1 (RC0452)


title: Muscle, myoblast, Rep7, siCtrl

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siCtrl-vs-siSirt1.csv
7_siCtrl

value: WT

value: siCtrl


title: ovarian cancer P0946


title: peripheral blood, colon polyps-r1 (RC0449)


title: stra8_het_captis_3

description:
stra8_het_captis_3_S3
Supplemental_Table_S4_5.xlsx

source_name: caput epididymis tissue

value: caput epididymis tissue


title: peripheral blood, colon polyps-r1 (RC0444)

value: peripheral blood


title: Muscle, myoblast, Rep4, siCtrl

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siCtrl-vs-siSirt1.csv
4_siCtrl


title: ovarian cancer P0962


title: peripheral blood, colon polyps-r1 (RC0447)

value: F


title: ovarian cancer P0941


title: stra8_het_captis_2

description:
stra8_het_captis_2_S2
Supplemental_Table_S4_5.xlsx


title: Muscle, myoblast, Rep3, siCtrl

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siCtrl-vs-siSirt1.csv
3_siCtrl


title: Muscle, myoblast, Rep2, siCtrl

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siCtrl-vs-siSirt1.csv
2_siCtrl


title: ovarian cancer P0934


title: stra8_het_captis_1

description:
stra8_het_captis_1_S1
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colon polyps-r1 (RC0443)

value: colon polyps


title: ovarian cancer P0927


title: peripheral blood, colon polyps-r1 (RC0432)

value: M


title: peripheral blood, colon polyps-r1 (RC0440)


title: Muscle, myoblast, Rep1, siCtrl

description:
150 bp sequencing
raw_counts_siCtrl-vs-Lmod1.csv
raw_counts_siCtrl-vs-siSirt1.csv
normalized_counts_siCtrl-vs-Lmod1.csv
normalized_counts_siCtrl-vs-siSirt1.csv
TPM_values_siCtrl-vs-siLmod1.csv
TPM_values_siCtrl-vs-siSirt1.csv
1_siCtrl


title: ovarian cancer P0920


title: defb_homo_cautis_3

description:
defb_homo_cautis_3_S29
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Defb41-iCre


title: defb_homo_cautis_4

description:
defb_homo_cautis_4_S30
Supplemental_Table_S4_5.xlsx


title: mouse Treg Hi-C

city: New York City

first: Christina

last: Leslie

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
scATAC-seq FASTQ files were aligned to hg38, hg19 or mm10 and counted by Cell Ranger ATAC v1.2.0 with default parameters.
For peak calling of the scATAC-seq data, filtered fragments for cells in each dataset/cell population were aggregated and used as input to the MACS2 peak caller (parameters -f BED, -g 2.7e9, -no-model, -shift -75, -extsize 150, -q 0.05). Peaks were filtered using an IDR cutoff of 0.05. Peaks within 500bp of each other were merged. A peak-by-cell count matrix was then created by ArchR.
Hi-C FASTQ files were aligned to mm10 genomes and reads that are duplicates or invalid ligation products were filtered out using the HiC-Pro pipeline (v3.1.0) with default settings.
Assembly: hg38/mm10
Supplementary files format and content: fragment files were generated by cellranger

source_name: spleen; peripheral and mesenteric lymph nodes

extract_protocol:
10x Genomics single cell multiome protocol for nuclei preparation for scATAC samples. Arima HiC+ kit (Arima Genomics, San Diego, CA) was used for Hi-C samples.
Single-cell Multiome libraries were generated with the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit following the manufacturer’s guidelines. The libraries were sequenced on the NovaSeq 6000 platform following the manufacturer’s guidelines. Hi-C library preparation follows Arima protocol modifications for Accel-NGS 2S DNA plus library kit (IDT, Coralville, IA). After end repair and ligation, libraries were quantified using the KAPA library quantification kit (Roche, Indianapolis, IN) and PCR amplified for the number of cycles required to generate >4nM per library. Hi-C libraries were sequenced on an Illumina NovaSeq and raw sequencing data in the Fastq format were obtained.

value: regulatory T cell


title: peripheral blood, colon polyps-r1 (RC0409)


title: peripheral blood, colon polyps-r1 (RC042)


title: ovarian cancer P0919

value: ovarian cancer


title: mouse GCB scATAC

library_source: genomic single cell

source_name: spleen

value: spleen

value: germinal center B cell


title: ovarian cancer P0917

value: primary tumor

value: HGSC


title: defb_homo_cautis_1

description:
defb_homo_cautis_1_S27
Supplemental_Table_S4_5.xlsx


title: defb_homo_cautis_2

description:
defb_homo_cautis_2_S28
Supplemental_Table_S4_5.xlsx


title: INPUT_8_CELL

city: Mumbai

first: Priyanka

last: Parte

state: Maharashtra

address: J.M.Street, Parel

department: Gamete Immunobiology

country: India

institute: ICMR-National Institute for Research in Reproductive and Child Health

data_processing:
raw reads were trimmed via Trimmomatic and aligned to Mus musculus mm10 genome using Bowtie2 (version 2.4.5)
PCR duplicates were filtered out via Picard (version 2.23.9)  and unmapped and non-uniquely mapped reads were removed via SAMtools (version 1.13)
TH2B peaks after comparing with respective Input controls were called using MACS version 2.2.7.1  with the parameters “–nolambda –nomodel – q-value cutoff - 0.05
Assembly: mm10/ GRCm38
Supplementary files format and content: BigWig files were created using ‘bamCoverage’ function of ‘deeptools package’ (version 3.5.1.0.0)31 (bin size: 50bps ;Scaling/Normalization method: rpkm; scaleFactor 1.0) in Galaxy server

source_name: 8 Cell embryos

extract_protocol:
Libraries were prepared using the Qiagen UltraLow Input Library Kit using the manufacturer’s instructions.Prepared libraries were sequenced on Illumina Novaseq to generate 60 M, 2x150 bp reads/sample
ultra-low-input native chromatin immunoprecipitation and sequencing (ULI-NChIP-seq)

value: 8 Cell embryos

value: None (Input sample)


title: defb_homo_captis_4

description:
defb_homo_captis_4_S26
Supplemental_Table_S4_5.xlsx

value: caput epididymal tissue


title: INPUT_2_CELL

source_name: 2- Cell embryos

value: 2- Cell embryos


title: ovarian cancer P0915

value: Serous carcinoma


title: INPUT_OOCYTE

source_name: MII-Oocyte

value: MII-Oocyte


title: ovarian cancer P0916


title: defb_homo_captis_3

description:
defb_homo_captis_3_S25
Supplemental_Table_S4_5.xlsx


title: ovarian cancer P0912


title: peripheral blood, colon polyps-r1 (RC0404)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

source_name: peripheral blood

value: peripheral blood


title: defb_homo_captis_2

description:
defb_homo_captis_2_S24
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colon polyps-r1 (RC0403)

value: F


title: ChIP_TH2B_8_CELL

value: anti-Histone H2B, testis variant antibody (Millipore, 07-680)


title: peripheral blood, colon polyps-r1 (RC0406)

value: M

value: colon polyps


title: ChIP_TH2B_2_CELL


title: defb_homo_captis_1

description:
defb_homo_captis_1_S23
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Defb41-iCre


title: ovarian cancer P0909

value: ovarian cancer


title: ovarian cancer P0908


title: defb_het_cautis_4

description:
defb_het_cautis_4_S22
Supplemental_Table_S4_5.xlsx

value: cauda epididymis tissue

value: Dgcr8+/fl; Defb41-iCre


title: ChIP_TH2B_OOCYTE


title: ovarian cancer P0906

value: primary tumor


title: CD8-cocultured2

city: Seoul

first: Jihyun

last: Kim

state: Seoul

address: 103 Daehak-ro, Jongno-gu, Seoul, Republic of Korea, 융합관 312

country: South Korea

institute: Seoul National University

data_processing:
Paired-end sequencing reads were produced using the Illumina NovaSeq platform. Prior to analysis, Trimmomatic v0.38 was employed to eliminate adapter sequences and trim bases exhibiting subpar quality.
The resulting clean reads were mapped to the Mus musculus (mm10) reference genome using HISAT v2.1.0, built upon HISAT2.
The reference genome sequence and gene annotation data were procured from the NCBI Genome assembly and NCBI RefSeq database, respectively.
The aligned data, available in SAM file format, underwent sorting and indexing utilizing SAMtools v1.9. Following alignment, transcripts were assembled and quantified via StringTie v2.1.3b.
Quantification was executed at both the gene and transcript levels, utilizing metrics such as raw read count.
Assembly: mm10
Supplementary files format and content: A text file includes the aligned read count per transcript for each sample

source_name: Spleen

extract_protocol:
Extract using Trizol reagent.
The RNA isolated from each sample was used to construct sequencing libraries with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Illumina, following the manufacturer's protocol.

value: Spleen

tag: cell line

value: Primary mouse cells

value: CD8 T cells

value: WT

value: Co-cultured


title: defb_het_cautis_3

description:
defb_het_cautis_3_S21
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colon polyps-r1 (RC0395)


title: ovarian cancer P0901

value: HGSC

value: Serous carcinoma


title: defb_het_cautis_2

description:
defb_het_cautis_2_S20
Supplemental_Table_S4_5.xlsx


title: CD8-cocultured1


title: peripheral blood, colon polyps-r1 (RC0399)

value: peripheral blood


title: defb_het_cautis_1

description:
defb_het_cautis_1_S19
Supplemental_Table_S4_5.xlsx


title: ovarian cancer P0895


title: peripheral blood, colon polyps-r1 (RC0384)

value: F


title: peripheral blood, colon polyps-r1 (RC0392)


title: peripheral blood, colon polyps-r1 (RC0402)


title: ovarian cancer P0893


title: peripheral blood, colon polyps-r1 (RC0381)


title: peripheral blood, colon polyps-r1 (RC0363)


title: peripheral blood, colon polyps-r1 (RC0362)


title: CD8_only1

value: Untreated


title: ovarian cancer P0892


title: defb_het_captis_3

description:
defb_het_captis_3_S17
Supplemental_Table_S4_5.xlsx

value: caput epididymis tissue


title: ILC2cocultured2

source_name: Lung

value: Lung

value: Type 2 Innate lymphoid cell


title: peripheral blood, colon polyps-r1 (RC030)

value: M

value: colon polyps


title: ovarian cancer P0888

value: ovarian cancer


title: ILC2cocultured1


title: ovarian cancer P0884

value: primary tumor


title: CD8_only2

value: Spleen


title: peripheral blood, colon polyps-r1 (RC029)


title: ovarian cancer P0882


title: ILC2-only2

value: Primary mouse cells


title: defb_het_captis_1

description:
defb_het_captis_1_S15
Supplemental_Table_S4_5.xlsx

value: Dgcr8+/fl; Defb41-iCre


title: defb_het_captis_4

description:
defb_het_captis_4_S18
Supplemental_Table_S4_5.xlsx


title: stra8_homo_cau_tis_8

description:
DgCAepi-4_S11
Supplemental_Table_S1_3.xlsx

data_processing:
For each small RNA library, reads were mapped to rRNAs, miRbase, murine tRNAs, piRNA clusters, to Repeatmasker, and Refseq using Bowtie 2.
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

extract_protocol:
Total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (18-40nts).
Illumina Tru-seq Small RNA Library

value: cauda epididymis tissue

value: Dgcr8fl/fl; Stra8-iCre


title: ILC2-only1

value: WT


title: ovarian cancer P0880

value: HGSC

value: Serous carcinoma


title: defb_het_captis_2

description:
defb_het_captis_2_S16
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colon polyps-r1 (PB3878)

value: peripheral blood

value: F


title: stra8_homo_cau_tis_7

description:
DgCAepi-3_S10
Supplemental_Table_S1_3.xlsx


title: RAW264.7 cells, control shRNA

city: Noda

first: Yasuhiro

last: Arasaki

state: Chiba

address: Yamazaki, 2641

department: Molucular Phamacology

institute: Tokyo University of Science

data_processing:
Illumina Novaseq software used for basecalling
Sequence reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using Hisat2.
Rea count extraction and normalization were perormed using python2.7.
Supplementary files format and content: mm10
Supplementary files format and content: Matrix table with gene counts for every gene and every sample after TMM normalization.

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using FastGene RNA Basic Kit (NIPPON genetics).
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: 7,500 cells/cm2 were seeded  in 12-well plates. After 24hr, we treated with 100 ng/ml RANKL.

value: RAW264.7 cells

value: macrophages

value: control

value: RANKL


title: RAw264.7 cells, Cpeb4 shRNA

value: Cpeb4 shRNA


title: peripheral blood, colon polyps-r1 (RC0246)

value: M

value: colon polyps


title: ovarian cancer P0873

value: ovarian cancer

value: primary tumor


title: stra8_homo_cau_tis_6

description:
DgCAepi-2_S9
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB3739)


title: ovarian cancer P0868


title: peripheral blood, colon polyps-r1 (PB3800)


title: stra8_homo_cau_tis_4

description:
dg2-ca-epi-4_S8
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (RC0276)


title: MUC63M1

city: Bunkyo-ku

first: Junya

last: Arai

state: Tokyo

address: Clinical reserch center A #422 7-3-1 Hongo

institute: University of Tokyo

data_processing:
RaNA (https://ranaseq.eu/contact)
Read count extraction and normalization were performed with RaNa website.
Assembly: mm10
Supplementary files format and content: Tab-delimited tsv file included raw counts for each samples.

source_name: gastric mucosa at corpus

extract_protocol:
RNA was harvested using the Nucleospin RNA kit (takara-bio).
RNA libraries for RNA sequence were prepared using TruSeq Stranded mRNA Library Prep kit.

value: gastric mucosa at corpus


title: stra8_homo_cau_tis_3

description:
dg2-ca-epi-3_S6
Supplemental_Table_S1_3.xlsx

value: cauda epididymis tissue


title: stra8_homo_cau_tis_5

description:
DgCAepi-1_S8
Supplemental_Table_S1_3.xlsx

value: Dgcr8fl/fl; Stra8-iCre


title: ovarian cancer P0867

value: Endometrioid carcinoma


title: Control2


title: ovarian cancer P0861

value: HGSC


title: stra8_homo_cau_tis_2

description:
dg2-ca-epi-2_S3
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0859

value: Serous carcinoma


title: stra8_homo_cau_tis_1

description:
dg2-ca-epi-1_S2
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB3389)

state: VA

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood


title: peripheral blood, colon polyps-r1 (PB3677)

value: F


title: Contro1


title: ovarian cancer P0879


title: MUC63M2


title: ovarian cancer P0854


title: peripheral blood, colon polyps-r1 (PB3323)


title: stra8_het_cau_tis_6

state: Pennsylvania

description:
hetCAepi-3_S14
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Stra8-iCre


title: MUC6KO2

source_name: gastric mucosa at antrum

value: gastric mucosa at antrum


title: peripheral blood, colon polyps-r1 (PB3004)


title: ovarian cancer P0853


title: peripheral blood, colon polyps-r1 (PB2932)


title: ovarian cancer P0850


title: stra8_het_cau_tis_4

description:
het2-ca-epi-4_S7
Supplemental_Table_S1_3.xlsx


title: stra8_het_cau_tis_5

description:
hetCAepi-1_S12
Supplemental_Table_S1_3.xlsx


title: WT3


title: MUC6KO1


title: WT2


title: ovarian cancer P0847


title: ovarian cancer P0846


title: stra8_het_cau_tis_3

description:
het2-ca-epi-3_S5
Supplemental_Table_S1_3.xlsx


title: MUC6KO3


title: peripheral blood, colon polyps-r1 (PB3019)


title: peripheral blood, colon polyps-r1 (PB2784)


title: peripheral blood, colon polyps-r1 (PB2726)


title: WT1


title: ovarian cancer P0844


title: Front foot, E17.5, rep3

city: Hangzhou

first: Liang

last: Gong

address: WenYi West Rd 1369

institute: Liangzhu Laboratory

data_processing:
RNA sequencing reads using trim_galore (v0.6.8) under flags: -q 20, --length 20, and –stringency 3
Clean reads were mapped to mm10 assembly by STAR (v2.7.10) aligner with parameters: -- alignSJoverhangMin 8, --alignSJDBoverhangMin 10, --alignSJDBoverhangMin 1, and --chimSegmentMin 15
Genes expression matrix was subsequently measured by htseq program (v0.11.1) under the flags: -m union and -s reverse
Read counts were normalized with fragments per kilobase per million mapped fragments (FPKM) for groups comparison
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts matrix of all samples as columns
Supplementary files format and content: comma-delimited text file includes FPKM normalized counts matrix of all samples as columns

source_name: ventral front foot

extract_protocol:
Total RNA was extracted using RNA extraction kit (Takara, Japan) and the concentration was determined using the NanoDrop ND-1000. 2 μg of total RNA per specimen was used to construct the RNA-seq library.
The RNA-seq libraries were prepared using a Illumina TruSeq RNA Sample Preparation Kit and sequenced on the Illumina NovaSeq 6000 platform with PE150 at Frasergen Bioinformatics.

value: ventral front foot

value: tissue


title: ovarian cancer P0837

source_name: primary tumor


title: peripheral blood, colon polyps-r1 (PB2383)


title: peripheral blood, colon polyps-r1 (PB2479)


title: stra8_homo_cap_tis_8

description:
DgCPepi-4_S18
Supplemental_Table_S1_3.xlsx

value: caput epididymis tissue


title: Front foot, E17.5, rep2


title: stra8_homo_cap_tis_7

description:
DgCPepi-3_S17
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0834


title: Front foot, E17.5, rep1


title: peripheral blood, colon polyps-r1 (PB2402)

value: M


title: Back, E15.5, rep3

source_name: dorsal back

value: dorsal back


title: stra8_homo_cap_tis_5

description:
DgCPepi-1_S15
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0831

value: ovarian cancer


title: stra8_homo_cap_tis_6

description:
DgCPepi-2_S16
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB2215)

value: colon polyps


title: Back, E15.5, rep2


title: stra8_het_cau_tis_1

description:
het2-ca-epi-1_S1
Supplemental_Table_S1_3.xlsx

source_name: cauda epididymis tissue


title: ovarian cancer P0830

value: primary tumor


title: peripheral blood, colon polyps-r1 (PB2118)


title: ovarian cancer P0827


title: Back, E15.5, rep1


title: peripheral blood, colon polyps-r1 (PB2172)


title: stra8_homo_cap_tis_4

description:
dg2-cp-epi-4_S16
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB1957)


title: ovarian cancer P0825


title: stra8_homo_cap_tis_3

description:
dg2-cp-epi-3_S14
Supplemental_Table_S1_3.xlsx


title: P14 CD8 T cells from draining lymph nodes after skin vaccinia-GP33 infection

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

description: 10x Genomics

data_processing:
The barcoded processing, gene counting were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol: P14 CD90.1 CD8 T cells were isolated from WT mouse draining lymph nodes of ears 45 days post ear infection with vaccinia-GP33. Draining lymph nodes were pooled from 7 mice. Mouse lymph nodes  were smashed on a 70um filter. Lymph node suspension was filtered and then cells were stained with CD90.1 PE. Cells were then enriched using Miltenyi magnetic enrichment kit. P14 T cells were then fluorescence activated cell sorted for CD90.1+ CD8+, CD45 intravenous negative, CD44+, DAPI-

value: Lymph node

value: CD8 T cell

tag: Sex

value: Female


title: ovarian cancer P0821

tag: tissue

value: HGSC


title: stra8_homo_cap_tis_2

description:
dg2-cp-epi-2_S11
Supplemental_Table_S1_3.xlsx

source_name: caput epididymis tissue

value: Dgcr8fl/fl; Stra8-iCre


title: EGCG treated replicate 2

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

institute: CSIR Centre for Cellular and Molecular biology

data_processing:
bcl2fastq v2.20 software used for basecalling
Read quality was checked for each sample using FastQC v0.11.9
Sequence reads were trimmed by cutadapt v2.8 and mapped to mm11 whole genome using STAR v2.7.1a with the following command:  STAR --runThreadN 16 --runMode alignReads --sjdbGTFfile ./Mus_musculus.GRCm39.105.gtf --limitBAMsortRAM 34000000000 --quantMode  GeneCounts --genomeDir  star_index/  --readFilesCommand zcat --outSAMstrandField intronMotif --readFilesIn file.1.fastq.gz  file.2.fastq.gz --outSAMtype BAM SortedByCoordinate  --outFileNamePrefix
Quantification of trancripts was done using RSEM v1.2.31
Assembly: mm11(GRCm39.105)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

extract_protocol:
Total RNA was extracted by RNeasy mini kit protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Library Prep Kit following manufacturer's protocols.

value: TRT

value: EGCG treated

tag: batch


title: EGCG treated replicate 3