title: BSseq MII oocytes vivo 6

description: Library name: vivo_24


title: C2C12, WT, rep3

status: Public on Jul 02 2025

type: SRA

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

library_source: transcriptomic

data_processing:
fastq.gz groomer tool  (https://usegalaxy.org)
BOWTIE2 v2.3.4.2  (https://usegalaxy.org)
featureCounts v1.6.3+galaxy2 (https://usegalaxy.org)
Assembly: mm10
Supplementary files format and content: DESeq2 v2.11.40.6+galaxy1 (https://usegalaxy.org)

molecule: total RNA

organism: Mus musculus

source_name: skeletal muscle cell line

growth_protocol: C2C12 control, C2C12 Hira KO and C2C12 Daxx KO cell lines were collected when grown in high serum medium at low density (proliferating conditions). C2C12 and Hira KO samples were previously deposited on: GSE161056. Here we deposit Daxx KO dataset and the dKO dataset with equivalent C2C12 control dataset.

extract_protocol:
C2C12 cells were collected for RNA extraction using Machery Nagel NucleoSpin RNA purification kit
Libraries were prepared with TruSeq Stranded Total RNA Sample preparation kit according to supplier recommendations. Briefly, the key stages of this protocol are successively, the removal of ribosomal RNA fraction from 1µg of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing

tag: tissue

value: skeletal muscle cell line

tag: cell line

tag: cell type

value: myoblasts

tag: genotype

value: WT


title: mucCRC016_RNA-seq

city: Daejeon

first: Jeewoo

last: Seo

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology, KRIBB

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.7.3a).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

organism: Homo sapiens

source_name: mucinous colorectal cancer tissue

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were assessed using the RNA Integrity Number (RIN).
TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA)

tag: disease state

value: Mucinous adenocarcinoma

tag: Sex

value: female

tag: age

tag: tumor stage

value: IIIB

value: mucinous colorectal cancer tissue


title: BSseq MII oocytes vivo 5

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description: Library name: vivo_23

library_source: genomic

data_processing:
We processed a total of 88 libraries (88 oocytes), adapting and quality-trimming them using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) for sequences with a Phred score of less than 20. Additionally, one negative control was sequenced to detect any technical issues. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using HiSat2 version 2.1.0 in single-end mode. For the cumulus cell samples, feature counting at the gene and transcript isoform level was done using rsem-calculate-expression (RSEM v1.3.3) (Li et al., 2011). Data processing was done in R (v4.2.2) using the edgeR (v3.38.4) package for differential gene expression analysis (Chen et al., 2016).
A total of 46 scBS-seq libraries were processed for analysis. The initial 6 base pairs, which included the N portion of the random primers, adapters, and low-quality bases (Phred score <20), were trimmed using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) in single-end mode. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using Bismark version 0.18.2 (Krueger & Andrews, 2011) in single-end and nondirectional mode, followed by deduplication and methylation calling through Bismark functions.
Assembly: Bos Taurus (UMD3.1_v91)
Supplementary files format and content: Normalized counts
Supplementary files format and content: 20CpG_windows_methylation

molecule: genomic DNA

organism: Bos taurus

source_name: MII oocytes

growth_protocol: For the collection of in vivo matured (IVO), in vitro matured (IVM) and in vivo + in vitro mature (VV) cumulus-oocytes complexes (COCs), four non-lactating and non-pregnant Holstein heifers (15 - 18 months of age) were used. For the collection of IVO and VV COCs, animals were synchronized using an intravaginal progesterone-releasing device (CIDR, Zoetis Belgium). Eight days later, the device was removed, and heifers received 2 mL (0.5 mg) of prostaglandin (PG; Cyclix Virbac, France). Estrus (=day 0) was confirmed two days later by ultrasound. To induce ovulation, 2.5 mL (10 µg) of Gonadotropin-releasing hormone (GnRH, Receptal, Intervet, Germany) was injected on day 8 of the estrous cycle. From day 10, animals were superovulated with 180 mg of follicle-stimulating hormone (FSH, Folltropin, Vetoquinol, Canada) administered twice daily for four days in decreasing doses. On day 12, animals received 3 mL (0.75 mg) of PG, and the luteinizing hormone (LH) surge was induced with 2.5 mL GnRH administered 40 h after  PG injection. Follicles ≥ 8mm in diameter were aspirated 24h after GnRH injection, using an 18 gauge needle. A 15-20 mL/min aspiration vacuum pressure was used due to the presence of expanded and sticky cumulus cells characteristic of oocyte maturation. Before follicle aspiration, the OPU tubing system was rinsed with polyvinylpyrrolidone (PVP) medium (0.3% PVP (PVP-360; Sigma) in Ca- and Mg-free PBS + 10 IU/mL heparin (Sigma)). The follicular content was collected in a 50 mL conical tube, and COCs were recovered under a stereomicroscope and stored in EmXcell medium without BSA (IMV-technologies, France) until the end of the collection procedure. After aspiration, COCs were collected under a stereomicroscope. Oocytes with evident cumulus expansion (IVO) were immediately denuded, whereas oocytes with poor cumulus expansion were submitted to IVM for 22 h (VV group), in groups (based on the cow of origin) in 50 µL bicarbonate-buffered TCM199 medium supplemented with gentamicin (50 mg/L) and epidermal growth factor (20 µl/mL). To assess maturation status, IVO and VV COCs were denuded individually in 0.1% hyaluronidase (Sigma) in PVP medium for approximately 2 min and by pipetting with a STRIPPER pipet holder and a 135-μm capillary (Origio, Cooper Surgical, CT, US) until all cumulus cells were removed from the oocyte. Denuded oocytes were classified as mature or immature oocytes based on the presence or absence of the polar body (PB), respectively. Mature IVO oocytes (n=28) and VV oocytes (n=20) were washed individually three times in PVP medium, treated with pronase to dissolve the zona pellucida (0.1% protease from S. griseus, in TCM-199), and immediately stored in 5 µl of Buffer RLT (Qiagen) at -80 °C until further use. Cumulus cells from IVO COCs were collected and pooled based on the cow of origin, and immediately stored in a lysis buffer for further analysis. For the collection of IVM oocytes, animals received GnRH (Receptal, Intervet, Germany) injection eight days after estrus and aspiration of follicles ≤ 8 mm was performed through an OPU procedure four days later. After aspiration, immature COCs (IVM group) were collected and underwent IVM as described above. After 22h, COCs were denuded, and mature oocytes (n=32) with their respective cumulus cells were processed and stored as described in the previous paragraph.

extract_protocol:
DNA and RNA from oocyte were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery. Total RNA was extracted from seven cumulus cells samples (four from in vivo matured, three from in vitro matured COCs) using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction. The RNA samples underwent quality and concentration assessments using an RNA 6000 Pico Chip (Agilent Technologies, Carlsbad, CA, USA).
ScRNA-seq and scBSseq

value: MII oocytes

value: Wild-type


title: SI_34511_R265-71del+/+;PbCre+_Case

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

country: USA

institute: University of Michigan

data_processing:
Read demultiplexing, alignment and gene quantification are conducted with the  Cell Ranger ARC pipeline (v2.0).  Custom reference was built by adding sequences of human FOXA1 and puroR to the prebuilt mouse reference (mm10)
Assembly: mm10
Supplementary files format and content: filtered feature matrix (.h5)
Library strategy: GEM Single-cell Multiome ATAC+Gene expression

source_name: prostate

growth_protocol: Mice were aged in a pathogen-free facility in compliance with IACUC prior to tissue harvest.

extract_protocol: Single-cell multiomics was performed using the Chromium Next GEM Single-cell Multiome ATAC+Gene expression kit (10x Genomics) according to the manufacturer’s protocol20. Briefly, nuclei were isolated, followed by transposition and adapter ligation using a Tn5 transposase. Transposed nuclei were loaded onto a Chromium Next GEM microfluidic chip along with gel beads containing 10x barcoded oligonucleotides. The GEMs were incubated to produce barcoded DNA from transposed chromatin (ATAC) and barcoded full-length cDNA from polyadenylated mRNA (Gene expression) within each GEM. Following this, the GEM is broken, cDNA is amplified, and pre-amplified cDNA is used as input for both the ATAC and gene expression library preparation. For ATAC, sample indexing primers are used for further amplification while the amplified cDNA underwent fragmentation, end repair, and A-tailing, followed by adapter ligation and PCR amplification to generate final sequencing libraries. Library quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: Mice were euthanized, and the distinct prostate lobes were microdissected.The lobes were then minced using a disposable scalpel into small pieces around one mm3 in a 10-cm culture dish under aseptic conditions. Subsequently, the minced tissues were transferred into 15 mL tubes containing prewarmed (37 °C) advanced DMEM F-12 +/+/+ media with 5 mg/mL of collagenase Type II (Gibco, 17101015) and incubated on a rotator for 1 hour at 37°C. Next, the tissues were digested with TrypLE (Thermo Fisher Scientific, 12605010) for 15 minutes, followed by a media wash. Single cells were strained using a 70 and 40-micron filter, followed by a 0.4% BSA in 1XPBS wash. Following this, cells were processed for single-cell RNA-sequencing using the  Chromium Next GEM Single Cell 3' kit v3.1 (10x Genomics).

value: prostate

value: mixed

value: male

tag: treatment

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene.   These animals were castrated for 4 weeks.


title: C2C12, WT, rep2


title: mucCRC015_RNA-seq

value: IIIC


title: SI_37330_Ms#3650_R265-71del+/+; Trp53f/f PbCre+_AD_Case

molecule: nuclear RNA

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene. Anterior and Dorsal lobes only


title: SI_34510_R265-71del+/+;PbCre-_Control

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.   These animals were castrated for 4 weeks.


title: BSseq MII oocytes vivo 3

description: Library name: vivo_21


title: mucCRC014_RNA-seq

value: IIA


title: C2C12, Daxx+Hira KO, rep3

value: skeletal muscle cell line

value: Daxx -/-; Hira -/-


title: C2C12, WT, rep1

value: myoblasts

value: WT


title: C2C12, Daxx+Hira KO, rep2


title: SI_34508_R265-71del+/+;Trp53+/+;PbCre-_Control

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. These animals were castrated for 4 weeks.


title: SI_34509_R265-71del+/+;Trp53+/+;PbCre+_Case

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene. These animals were castrated for 4 weeks.


title: mucCRC018_RNA-seq

value: Mucinous adenocarcinoma

value: mucinous colorectal cancer tissue


title: BSseq MII oocytes vivo 4

description: Library name: vivo_22

value: MII oocytes

value: Wild-type


title: BSseq MII oocytes vivo 2

description: Library name: vivo_20


title: mucCRC013_RNA-seq


title: SI_34507_R265-71del+/+;PbCre+_Case

value: prostate

value: mixed


title: mucCRC010_RNA-seq

value: male

value: IIIB


title: mucCRC012_RNA-seq


title: mucCRC011_RNA-seq


title: C2C12, Daxx KO, rep2

data_processing:
alignment: BWA algorithm (mem mode; default settings)
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file and with the –nomodel option
Assembly: mm10
Supplementary files format and content: Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program

growth_protocol: C2C12 control, C2C12 Hira KO and C2C12 Daxx KO cell lines were collected when grown in high serum medium at low density (proliferating conditions). C2C12 and Hira KO samples were previously deposited on: GSE161056

extract_protocol:
C2C12 cells were harvested and cell pellets were resuspended in lysis buffer, pelleted and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems)

value: Daxx -/-


title: C2C12, Daxx+Hira KO, rep1


title: BSseq MII oocytes vitro 18

description: Library name: vitro_18


title: BSseq MII oocytes vivo 1

description: Library name: vivo_19


title: SI_34506_R265-71del+/+;PbCre-_Control

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. These animals were castrated for 4 weeks.


title: BSseq MII oocytes vitro 17

description: Library name: vitro_17


title: mucCRC009_RNA-seq

value: IIA


title: Ms_3888_5ul_CRE_sgNSD2_10_60hFM_Rep2

description: Library name: SI_39215_Ms3888_5ul_CRE_sgNSD2_10_60hFM_Rep2

data_processing:
Alignment was  performed using kalliso (v0.46.1) quant to the mouse (mm10/GRCm38) or human (hg38/GRCh38) references. Read counts were adjusted for normalization and filtered in R via package EdgeR. Package Limma-Voom (vlimma_3.53.10) was involved for differential expression analysis. GSEA analysis and corresponding heatmaps and figures were created using R package fgsea (vfgsea_1.24.0), ComplexHeatmap and ggplot2 for signatures from MSigDB’s hallmark MTORC1 and custom AR signatures based on our data.
Assembly: mm10
Supplementary files format and content: counts matrix

growth_protocol: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by harvest or a further 12-hour starvation in media lacking EGF and DHT.

extract_protocol:
Total RNA was then isolated using QIAzol Lysis Reagent (QIAGEN) and extracted using the miRNeasy Mini Kit (Qaigen), with the inclusion of the on-column genomic DNA digestion step using the RNase-free DNase Kit (Qaigen), following the standard protocols. RNA was quantified using the NanoDrop 2000 Spectrophotometer (ThermoFisher Scientific), and 1 μg of total RNA was used for complementary DNA (cDNA) synthesis using the SuperScript III Reverse Transcriptase enzyme (Thermo Fisher Scientific) following the manufacturer’s instructions.
RiboErase RNA-seq libraries were prepared using 200–1,000 ng of total RNA extracted from mouse organoids. Ribosomal RNA was eliminated through enzymatic digestion of the specific probe-bound duplex rRNA using the KAPA RNA Hyper+RiboErase HMR kit (Roche). The remaining RNA was then fragmented to approximately 200-300 bp by heat treatment in fragmentation buffer. Following fragmentation, double-stranded cDNA was synthesized, and end-repair and ligation procedures were carried out using New England Biolabs (NEB) adapters. The final library preparation involved amplification using the 2x KAPA HiFi HotStart mix and NEB dual barcodes, following the manufacturer's protocol. Library quality was assessed using an Agilent 2100 Bioanalyzer to determine product size and concentration. Paired-end sequencing was performed on the Illumina HiSeq 2500 platform, with 2 × 100 nucleotide read lengths and sequence coverage of 15–20 million paired reads per sample.

treatment_protocol: For DHT stimulation experiments, cells were treated with 10nM of DHT for 24 hours.

value: 3888 (Del+/+; Trp53f/f)  prostate organoid

value: Prostate organoid oligoclone treated with sgNSD2 guides were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media


title: SI_33647_Ms#2990_P358fsA+/-;PbCre+ DVL_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: mucCRC008_RNA-seq


title: SI_33646_Ms#2987_P358fsA+/-;PbCre+ Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.  Anterior lobes only.


title: BSseq MII oocytes vitro 16

description: Library name: vitro_16


title: mucCRC006_RNA-seq

value: female


title: mucCRC007_RNA-seq

value: IIIC


title: SI_33645_Ms#2987_P358fsA+/-;PbCre+ DVL_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: mucCRC005_RNA-seq

value: Mucinous adenocarcinoma

value: mucinous colorectal cancer tissue


title: Ms_3888_5ul_CRE_sgNC_5_60hFM_Rep1

description: Library name: SI_39210_Ms3888_5ul_CRE_sgNC_5_60hFM_Rep1

value: Prostate organoid oligoclone treated with sgNC guides were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media


title: C2C12, Daxx KO, rep1

value: skeletal muscle cell line

value: myoblasts


title: BSseq MII oocytes vitro 15

description: Library name: vitro_15

value: MII oocytes

value: Wild-type


title: mucCRC004_RNA-seq

value: male


title: Ms_3132_CRE_NoED_Rep1

description: Library name: SI_31602 3132 CRE R1_NoED

value: prostate

value: 3132(R265-71del+/+) mouse prostate organoid

value: mixed

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: Ms_3888_5ul_CRE_sgNC_5_60hFM_Rep2

description: Library name: SI_39211_Ms3888_5ul_CRE_sgNC_5_60hFM_Rep2

value: 3888 (Del+/+; Trp53f/f)  prostate organoid


title: BSseq MII oocytes vitro 11

description: Library name: vitro_11


title: SI_33648_Ms#2990_P358fsA+/-;PbCre+ Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.  Anterior lobes only.


title: BSseq MII oocytes vitro 14

description: Library name: vitro_14


title: BSseq MII oocytes vitro 13

description: Library name: vitro_13


title: SI_33642_Ms#2988_P358fsA+/-;PbCre- Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Anterior lobes only.


title: SI_33641_Ms#2988_P358fsA+/-;PbCre- DVL_Prostate


title: Ms_3132_CRE_NoED_Rep2

description: Library name: SI_31603_3132 CRE R2_NoED


title: mucCRC003_RNA-seq

value: female

value: IIIB


title: SI_33643_Ms#2989_P358fsA+/-;PbCre- DVL_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: Ms_3132_Ctrl_NoED_Rep1

description: Library name: SI_31600_3132 Ctrl R1_NoED


title: Ms_3132_Ctrl_NoED_Rep2

description: Library name: SI_31601 3132 Ctrl R2_NoED


title: Ms_3888_5ul_CRE_sgNSD2_10_60hFM_Rep1

description: Library name: SI_39214_Ms3888_5ul_CRE_sgNSD2_10_60hFM_Rep1

value: Prostate organoid oligoclone treated with sgNSD2 guides were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media


title: SI_33640_Ms#2990_P358fsA+/-;PbCre+ Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Anterior lobes only.


title: mucCRC001_RNA-seq

value: Mucinous adenocarcinoma

value: IV

value: mucinous colorectal cancer tissue


title: BSseq MII oocytes vitro 9

description: Library name: vitro_9

value: MII oocytes

value: Wild-type


title: SI_33639_Ms#2990_P358fsA+/-;PbCre+ DVL_Prostate

value: prostate

value: male

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: SI_33644_Ms#2989_P358fsA+/-;PbCre- Anterior_Prostate

value: mixed


title: BSseq MII oocytes vitro 12

description: Library name: vitro_12


title: Ms_1947_CRE_Ar

description: Library name: SI_40292_1947_CRE_Ar

data_processing:
Reads were first processed using Trimmomatic version 0.39 (settings TruSeq3-PE-2.fa:2:30:10, minlen 50) followed by alignment with bwa (“bwa mem”, options -5SP -T0, version 0.7.17-r1198-dirty) to mm10 (GRCm38) genome reference or hg38 (GRCh38) reference. After alignment the reads were filtered using Markduplicates from Picard then by quality score of >20 via samtools. MACS2 was used to call peaks which were then filtered using bedtools and converted to bigwigs with UCSC wigtoBigwig. Cistrome overlap analysis were performed in R (v3.6.0) using ChipSeekAnno (v3.0.0) and ChipSeeker (v1.29.1). Enrichment heatmaps were generated using Deeptools. HOMER was used to perform motif enrichment analysis. Motif dot plot summaries were created in R (v3.6.0) using Sushi.
Assembly: mm10, hg38
Supplementary files format and content: .bed: peak locations from macs bed calling with blacklist removed; .bw: signal files

growth_protocol: Prostate organoids were seeded at a density of 30,000 cells/well and grown for 3-5 days in complete media.

extract_protocol:
500,000 to 1 million cells were used per ChIP reaction with 2ug of antibody. Briefly, cells were crosslinked for 10 minutes in a 1% formaldehyde solution, followed by termination with 1/10th the volume of 1.25M glycine for 5 minutes at room temperature. Following this, the cells were lysed and sonicated (Bioruptor Pico, Diagenode) with a desired chromatin size of about 200bp. Sheared chromatin was then incubated with desired antibodies overnight at 4 °C. Next day, the ChIP-DNA was de-crosslinked and purified using the Diagenode iPure Kit V3, following the manufacturer's protocol.
Utilizing the manufacturer’s instructions (Illumina), purified DNA was prepared for sequencing. About 1-10ng of ChIP DNA were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). Klenow fragment (3′ to 5′ exo minus; NEB) was used to add a single adenine base to fragment ends, followed by ligation of Illumina adaptors (Quick ligase, NEB). PCR enriched the adaptor-ligated DNA fragments using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Quantified libraries quality-checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: Organoids were stimulated with 1nM of R1881 for 6 hours before harvest. Organoids were dissociated using TrypleLE for 10 minutes and divided into 500,000 to 1 million cells per tube.Chromatin immunoprecipitation (ChIP) experiments were performed using the Ideal ChIP-seq kit for transcription factors (Diagenode) per the manufacturer’s protocol.

value: 1947 (P358fs+/-) prostate organoid

value: Cre+ virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. AR ChIP-seq was performed.


title: MTCRT537_RNA-seq

value: IIIC


title: mucCRC002_RNA-seq

value: IIA


title: BSseq MII oocytes vitro 8

description: Library name: vitro_8


title: SI_33638_Ms#2987_P358fsA+/-;PbCre+ Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.  Anterior lobes only.


title: BSseq MII oocytes vitro 10

description: Library name: vitro_10


title: HRCRC3977_RNA-seq

value: female


title: SI_33636_Ms#2989_P358fsA+/-;PbCre- Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Anterior lobes only.


title: BSseq MII oocytes vitro 5

description: Library name: vitro_5


title: Ms_3888_sgNC_5_Ar

description: Library name: SI_40293_3888_sgNC_5_Ar

value: 3888 (Del+/+; Trp53f/f)  prostate organoid

value: Cre+ virus and sgNC treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. AR ChIP-seq was performed.


title: HRCRC3928_RNA-seq

value: Mucinous adenocarcinoma

value: IIB


title: Ms_1706_CRE_CST

description: Library name: SI_35835_1706_CRE_CST

value: 1706 (R261G+/+) prostate organoid

value: Cre+ virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Mutant Foxa1 ChIP-seq was performed.


title: Ms_1947_control_Ar

description: Library name: SI_40291_1947_control_Ar

value: prostate

value: Cre- virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. AR ChIP-seq was performed.


title: BSseq MII oocytes vitro 6

description: Library name: vitro_6

value: MII oocytes

value: Wild-type


title: Ms_3888_sgNsd2_10_Ar

description: Library name: SI_40294_3888_sgNsd2_10_Ar

value: mixed

value: Cre+ virus and sgNsd2 treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. AR ChIP-seq was performed.


title: BSseq MII oocytes vitro 7

description: Library name: vitro_7


title: SI_33635_Ms#2989_P358fsA+/-;PbCre- DVL_Prostate

value: male

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: HRCRC3938_RNA-seq

value: mucinous colorectal cancer tissue


title: SI_33633_Ms#2988_P358fsA+/-;PbCre- DVL_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: SI_33634_Ms#2988_P358fsA+/-;PbCre- Anterior_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Anterior lobes only.


title: HRCRC3917_RNA-seq

value: female

value: IVA


title: BSseq MII oocytes vitro 4

description: Library name: vitro_4


title: Ms_1706_control_TFS

description: Library name: SI_35836_1706_control_TFS

value: Cre- virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Mutant Foxa1 ChIP-seq was performed.


title: BSseq MII oocytes vitro 2

description: Library name: vitro_2


title: Ms_1947_CRE_TFS

description: Library name: SI_30955_CRETFS_1947

value: 1947 (P358fs+/-) prostate organoid

value: Cre+ virus teated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Mutant Foxa1 ChIP-seq was performed.


title: SI_32183_Ms#3167_P358fsC+/-; Pten+/- ;PbCre- DVL_Prostate

value: P358fsC+/-; Pten+/- ;PbCre-


title: SI_33637_Ms#2987_P358fsA+/-;PbCre+ DVL_Prostate

value: prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: Ms_3888_sgNsd2_10_H3K36me2_CST

description: Library name: SI_40297_3888_sgNsd2_10_H3K36me2_CST

value: 3888 (Del+/+; Trp53f/f)  prostate organoid

value: Cre+ virus and sgNsd2 treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest.H3K36me2 ChIP-seq was performed.


title: HRCRC3805_RNA-seq

value: Mucinous adenocarcinoma

value: IIIC


title: HRCRC3963_RNA-seq

value: male


title: BSseq MII oocytes vitro 1

description: Library name: vitro_1

value: MII oocytes

value: Wild-type


title: SI_32182_Ms#3312_R265-71del+/-; PbCre- DVL_Prostate

value: mixed

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: HRCRC3792_RNA-seq

value: mucinous colorectal cancer tissue


title: Ms_3888_sgNC_5_H3K36me2_CST

description: Library name: SI_40296_3888_sgNC_5_H3K36me2_CST

value: Cre+ virus and sgNC treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. H3K36me2 ChIP-seq was performed.


title: BSseq MII oocytes vitro 3

description: Library name: vitro_3


title: SI_32181_Ms#3289_P358fsC+/-; Pten+/- ;PbCre- DVL_Prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: RNA-seq_HIGM1_patient_2

city: Beijing

first: changchang

last: cao

state: China

address: Datun, 15

country: China

institute: IBP

description: Library name: Sample 4

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
For CLIP-seq, UMIs were first trimmed and added to the name of read names. After removing adaptor sequences, CLIP-seq reads longer than 18nt were mapped to the reference mouse genome (mm10) with Bowtie. Duplicated reads were collapsed based on both UMIs and mapping positions.
For RNA-seq, paired-end clean reads were aligned to this reference genome using HISAT2 software (version 2.0.5). FeatureCounts (version 1.5.0) was then employed to enumerate reads mapped to each gene. Following this, an FPKM value of each gene was calculated, factoring in both the gene's length and the read count mapped to it. Differential gene expression between Bcas2-cKO and control mice, healthy person and HIGM1 patients (comprising a biological replicate per condition) were conducted using the DESeq2 R package (version 1.20.0). Genes demonstrating a padj value <= 0.05, as identified by DESeq2, were delineated as differentially expressed.
Assembly: mm10, hg38
Supplementary files format and content: bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software

source_name: Blood

growth_protocol: The primary B cells were cultured in RPMI1640 medium supplemented with 10% FBS and 100U of Penicillin-Streptomycin in 5% CO2 incubator at 37℃.

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, the 100000000 isolated B cells were irradiated at 400mJ/cm2 with 254nm UV light. The crosslinked cells were lysed and 15ug of BCAS2 (Abmart, Catalog # PA2466S) specific antibody was applied to pull-down protein-RNA complexes. After micrococcal nuclease treatment, 3’RNA linker ligation and 5’end 32P labeling, the immunoprecipitated complexes were fractionated on 10% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The auto-radiographed BCAS2 smear bands were cut and treated with Proteinase K to extract respective RNA by phenol and chloroform. The isolated RNA was then added a 5’ RNA linker and reverse transcribed by superscript reverse transcriptase III (life technologies, catalog# 18080-051). The PCR products were sequenced with illumina Hiseq 2500 platform. RNA-seq was performed as follows. Total RNA of B cells was extracted by Trizol while RNA from human peripheral blood mononuclear cells was extracted by using RNA extraction kit (Tiangen, Catalog # A0801A). mRNA from B cells and peripheral blood mononuclear cells was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, a transcriptome sequencing library was established. Utilizing a TruSeq PE Cluster kit v3-cBot-HS (Illumina) on a cBot Cluster Generation System, index-coded samples were clustered in strict accordance with the manufacturer’s guidelines. Upon completion of the clustering process, the library preparations were subjected to sequencing on the Illumina NovaSeq platform, generating 150 bp paired-end reads. Rigorous quality control measures were implemented post-sequencing to ensure that downstream analyses were performed exclusively on pristine, high-quality data.

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days.

value: Blood

value: peripheral blood mononuclear cells

value: High IgM Syndrome type I

value: No treatment


title: SI_32176_Ms#3167_P358fsC+/-; Pten+/- ;PbCre- DVL_Prostate

value: prostate

value: P358fsC+/-; Pten+/- ;PbCre-


title: HRCRC3735_RNA-seq

value: IIIB


title: RNA-seq_Healthy_person_2

description: Library name: Sample 2

value: Control


title: HRCRC3717_RNA-seq

value: Mucinous adenocarcinoma

value: IIIC


title: HRCRC3725_RNA-seq

value: male

value: IIA


title: RNA-seq_Healthy_person_1

description: Library name: Sample 1


title: SI_32175_Ms#3312_R265-71del+/-; PbCre- DVL_Prostate

value: mixed


title: RNA-seq_HIGM1_patient_1

description: Library name: Sample 3


title: FBb1-15

city: Boston

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

description:
Library name: FBb1-15
RNA CCs Cauda B1 LPS 3

data_processing:
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for one or more samples.
Assembly: mm9

source_name: epididymis

extract_protocol:
The RNA was isolated using PicoRNA KIT (Thermo Fisher Scientific).
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.

value: epididymis

value: Clear cells (CCs) isolated from CAUDA 1h after intravasal epididymal injection of LPS (25ug)

value: Transgenic mice that express EGFP under the control of the ATP6V1B1 gene promoter

value: LPS

tag: batch


title: FBb1-18

description:
Library name: FBb1-18
RNA CCs Cauda B1 Saline 3

value: Clear cells (CCs) isolated from CAUDA 1h after intravasal epididymal injection of saline

value: saline


title: FBb1-17

description:
Library name: FBb1-17
RNA CCs Corpus B1 Saline 3

value: Clear cells (CCs) isolated from CORPUS 1h after intravasal epididymal injection of saline


title: SI_32174_Ms#3289_P358fsC+/-; Pten+/- ;PbCre- DVL_Prostate

value: P358fsC+/-; Pten+/-;PbCre-

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: HRCRC3873_RNA-seq

value: mucinous colorectal cancer tissue


title: HRCRC3714_RNA-seq

value: IIIB


title: FBb1-16

description:
Library name: FBb1-16
RNA CCs IS/Caput B1 Saline 3

value: Clear cells (CCs) isolated from IS/CAPUT 1h after intravasal epididymal injection of saline


title: SI_32168_Ms#3314_R265-71del+/+;PbCre-DVL_Prostate

value: prostate

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: HRCRC3909_RNA-seq

source_name: non-mucinous colorectal cancer tissue

value: Non-mucinous adenocarcinoma

value: male

value: IV

value: non-mucinous colorectal cancer tissue


title: FBb1-14

description:
Library name: FBb1-14
RNA CCs Corpus B1 LPS 3

value: epididymis

value: Clear cells (CCs) isolated from CORPUS 1h after intravasal epididymal injection of LPS (25ug)


title: HRCRC3663_RNA-seq

value: Mucinous adenocarcinoma

value: IIA


title: HRCRC3726_RNA-seq


title: FBb1-13

description:
Library name: FBb1-13
RNA CCs IS/Caput B1 LPS 3

value: Clear cells (CCs) isolated from IS/CAPUT 1h after intravasal epididymal injection of LPS (25ug)

value: Transgenic mice that express EGFP under the control of the ATP6V1B1 gene promoter

value: LPS


title: SI_32167_Ms#3311_R265-71del+/+;PbCre+DVL_Prostate

value: mixed

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: HRCRC3462_RNA-seq

value: female

value: IIC

value: mucinous colorectal cancer tissue


title: HRCRC3711_RNA-seq


title: SI_32166_Ms#3310_R265-71del+/+;PbCre+DVL_Prostate

value: prostate


title: HRCRC3453_RNA-seq

value: IIIB


title: FBb1-12

description:
Library name: FBb1-12
RNA CCs Cauda B1 Saline 2

value: Clear cells (CCs) isolated from CAUDA 1h after intravasal epididymal injection of saline

value: saline


title: SI_32164_Ms#3314_R265-71del+/+;PbCre-DVL_Prostate

value: male

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: FBb1-11

description:
Library name: FBb1-11
RNA CCs Corpus B1 Saline 2

value: epididymis

value: Clear cells (CCs) isolated from CORPUS 1h after intravasal epididymal injection of saline


title: HRCRC3528_RNA-seq

value: Non-mucinous adenocarcinoma

value: IV

value: non-mucinous colorectal cancer tissue


title: HRCRC3410_RNA-seq

value: Mucinous adenocarcinoma


title: HRCRC3479_RNA-seq


title: SI_32163_Ms#3311_R265-71del+/+;PbCre+DVL_Prostate

value: mixed


title: HRCRC3375_RNA-seq


title: FBb1-10

description:
Library name: FBb1-10
RNA CCs IS/Caput B1 Saline 2

value: Clear cells (CCs) isolated from IS/CAPUT 1h after intravasal epididymal injection of saline

value: Transgenic mice that express EGFP under the control of the ATP6V1B1 gene promoter


title: HRCRC3379_RNA-seq

value: female

value: IIIC


title: FBb1-8

description:
Library name: FBb1-8
RNA CCs Corpus B1 LPS 2

value: Clear cells (CCs) isolated from CORPUS 1h after intravasal epididymal injection of LPS (25ug)

value: LPS


title: FBb1-7

description:
Library name: FBb1-7
RNA CCs IS/Caput B1 LPS 2

value: Clear cells (CCs) isolated from IS/CAPUT 1h after intravasal epididymal injection of LPS (25ug)


title: SI_32162_Ms#3310_R265-71del+/+;PbCre+DVL_Prostate

value: prostate

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene. Dorsal, Ventral and Lateral lobes only.


title: FBb1-9

description:
Library name: FBb1-9
RNA CCs Cauda B1 LPS 2

value: Clear cells (CCs) isolated from CAUDA 1h after intravasal epididymal injection of LPS (25ug)


title: SI_31637_3153:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre+

value: male

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.


title: SI_31638_3162:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre+


title: HRCRC3314_RNA-seq

value: IIA

value: mucinous colorectal cancer tissue


title: HRCRC3186_RNA-seq

value: Non-mucinous adenocarcinoma

value: non-mucinous colorectal cancer tissue


title: HRCRC3109_RNA-seq

value: Mucinous adenocarcinoma

value: IV


title: HRCRC3724_RNA-seq


title: HRCRC3946_RNA-seq

value: IIIB


title: SI_31636_3157:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre-

value: mixed

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.


title: HRCRC3290_RNA-seq


title: iMSC-P8-3

first: Wenpeng

last: Song

state: Beijing

address: Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

department: Department of Stomatology

institute: Capital Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: PSCs-derived mesenchymal stem cells

extract_protocol:
Total RNA was extracted from cells using the TRIzolTM reagent according to the manufacturer’s instructions. The RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). To construct RNA-seq libraries, mRNA was enriched using Oligo dT-attached magnetic beads, fragmented, and reverse-transcribed into cDNA.
The cDNA was then ligated to sequencing adapters, and PCR amplification was performed to enrich the libraries. After the library construction was completed, the library was initially quantified using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Massachusetts, USA) and then diluted to 1.5 ng/µL. The insert size of the library was subsequently analyzed using the Agilent 2100 Bioanalyzer. Once the insert size met the expected criteria, the effective concentration of the library was accurately determined using qRT-PCR (with the effective concentration being higher than 1.5 nM) to ensure the quality of the library. After the library passed quality control, different libraries were pooled according to their effective concentration and the required target data output for sequencing. The pooled libraries were then subjected to Illumina sequencing.

value: PSCs-derived mesenchymal stem cells


title: FBb1-6

description:
Library name: FBb1-6
RNA CCs Cauda B1 Saline

value: epididymis

value: Clear cells (CCs) isolated from CAUDA 1h after intravasal epididymal injection of saline

value: Transgenic mice that express EGFP under the control of the ATP6V1B1 gene promoter

value: saline


title: SI_31635_3159:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre-

value: prostate


title: HRCRC3937_RNA-seq

value: female


title: FBb1-5

description:
Library name: FBb1-5
RNA CCs Corpus B1 Saline

value: Clear cells (CCs) isolated from CORPUS 1h after intravasal epididymal injection of saline


title: iMSC-P8-2


title: FBb1-4

description:
Library name: FBb1-4
RNA CCs IS/Caput B1 Saline

value: Clear cells (CCs) isolated from IS/CAPUT 1h after intravasal epididymal injection of saline


title: SI_31634_3162:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre+

value: male

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have  expression of the transgene.


title: HRCRC3910_RNA-seq

value: Non-mucinous adenocarcinoma

value: IIIC

value: non-mucinous colorectal cancer tissue


title: iMSC-P8-1


title: HRCRC3861_RNA-seq

value: IIA


title: iMSC-P6-2


title: SI_31633_3153:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre+

value: mixed


title: FBb1-3

description:
Library name: FBb1-3
RNA CCs Cauda B1 LPS

value: Clear cells (CCs) isolated from CAUDA 1h after intravasal epididymal injection of LPS (25ug)

value: LPS


title: HRCRC3817_RNA-seq

value: IV


title: SI_31631_3159:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre-

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.


title: HRCRC3777_RNA-seq


title: iMSC-P6-1

value: PSCs-derived mesenchymal stem cells


title: FBb1-2

description:
Library name: FBb1-2
RNA CCs Corpus B1 LPS

value: epididymis

value: Clear cells (CCs) isolated from CORPUS 1h after intravasal epididymal injection of LPS (25ug)

value: Transgenic mice that express EGFP under the control of the ATP6V1B1 gene promoter


title: SI_30746_2723/25MsDVLprostate:P358fs-/-Cre-(ctrl)

value: prostate

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: HRCRC3696_RNA-seq

value: female


title: Ms3888_5ul_Ctrl_36h_NoED_Rep1

growth_protocol: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.

value: 3888 (Del+/+; Trp53f/f)  prostate organoid

value: male


title: FBb1-1

description:
Library name: FBb1-1
RNA CCs IS/Caput B1 LPS

value: Clear cells (CCs) isolated from IS/CAPUT 1h after intravasal epididymal injection of LPS (25ug)


title: Ms3888_5ul_Ctrl_36h_NoED_Rep2

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: SI_30745_2722/24MsDVLprostate:P358fs+/-Cre+(case)

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: Namalwa-XMU-0.3-1

city: Moscow

first: Elizaveta

last: Pankratova

address: Vavilov str., 32

department: Transcription factors

country: Russia

institute: Engelhardt Instittute of Molecular Biology^ Russian Academy of Sciense

data_processing:
Preliminary filtering of reads by length and quality, as well as removal of adapter sequences, was carried out using TrimGalore and Cutadapt
FASTQ files were obtained using bcl2fastq v2.20 Conversion Software (Illumina)
The Ensembl GRCh38 -103 assembly with masked repeat sequences and Ensembl annotation was used as the reference genome of Homo sapiens.
Mapping of reads to the reference genome was carried out using HiSat2
Expression levels were calculated using HTSeq package programs. The resulting expression matrices were analyzed using the DESeq2 library; genes with less than 10 reads were not used in the analysis.
Assembly: Ensembl GRCh38 -103 assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: lymphpblast

growth_protocol: Cells were maintained in DMEM with 10% FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin, in the 5% CO2 at 37C.

extract_protocol:
mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) was used with 3 ug of total RNA for sequencing library construction. RNA libraries were prepared using the standard Illumina protocols. Double-stranded cDNA, ligation reaction products, and PCR reaction products were purified using the AgencourtAMPure XP beads.

treatment_protocol: 2.5 µM XMU-MP-1 or 0.3 µM XMU-MP-1 72h in complete culture medium

value: lymphpblast

value: Namalwa

value: B lymphpblast

value: WT

value: XMU-MP-1 0.3 µM


title: SI_30747_2722/24MsDVLprostate:P358fs+/-Cre+(case)

value: mixed


title: Namalwa-XMU-2.5-2

value: XMU-MP-1 2.5 µM


title: HRCRC3874_RNA-seq

value: Non-mucinous adenocarcinoma

value: IIIA

value: non-mucinous colorectal cancer tissue


title: Ms3888_5ul_CRE_36h_NoED_Rep2

value: prostate


title: HRCRC3821_RNA-seq

value: female

value: IIIC


title: HRCRC3870_RNA-seq

value: male

value: IIIB


title: SI_31632_3157:FOXA1 R265-71del+/+,TP53+/+,Pb-Cre-

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.


title: Ms#3650_R265-71del+/+; Trp53f/f PbCre+_AD_Case_Lib2

library_source: transcriptomic single cell

data_processing:
Read demultiplexing, alignment and gene quantification are conducted with the 10X Genomics Cell Ranger pipeline (v7.1). Custom reference was built by adding sequences of human FOXA1 and puroR to the prebuilt mouse reference (mm10)
SI_37328 and SI_37335 are marked Lib1 and Lib2 as the data was sequenced independantly for these but for all computational purposes they were merged and treated as 1 library.
Assembly: mm10
Supplementary files format and content: filtered feature matrix (.h5)

growth_protocol: Mice were aged in for 100 weeks prior to tissue harvest in a pathogen-free facility in compliance with IACUC. Anterior and dorsal prostates were utilized for this experiment.

extract_protocol: Briefly, single-cell suspensions were loaded onto a Chromium Next GEM Chip along with reverse transcription reagents and Gel Beads containing barcoded oligonucleotides. The chip was then placed in a Chromium Controller to generate Gel Bead-in-Emulsions (GEMs), encapsulating individual cells with unique barcoded Gel Beads. Within each GEM, cellular mRNAs were reverse transcribed to generate barcoded full-length cDNA. Following reverse transcription, the GEMs were broken, and the barcoded cDNA was amplified by PCR. The amplified cDNA underwent fragmentation, end repair, and A-tailing, followed by adapter ligation and PCR amplification to generate final sequencing libraries. Library quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: Mice were euthanized, and the distinct prostate lobes were microdissected.The lobes were then minced using a disposable scalpel into small pieces around one mm3 in a 10-cm culture dish under aseptic conditions. Subsequently, the minced tissues were transferred into 15 mL tubes containing prewarmed (37 °C) advanced DMEM F-12 +/+/+ media with 5 mg/mL of collagenase Type II (Gibco, 17101015) and incubated on a rotator for 1 hour at 37°C. Next, the tissues were digested with TrypLE (Thermo Fisher Scientific, 12605010) for 15 minutes, followed by a media wash. Single cells were strained using a 70 and 40-micron filter, followed by a 0.4% BSA in 1XPBS wash. Following this, cells were processed for single-cell RNA+ATAC-sequencing using the  Chromium Next GEM Single-cell Multiome ATAC+Gene expression kit (10x Genomics).

value: R265-71del+/+; Trp53f/f PbCre+

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene.Anterior and Dorsal lobes only from 100-week old animals.


title: SI_30744_2723/25MsDVLprostate:P358fs-/-Cre-(ctrl)

value: Mice with conditional overexpression of the FOXA1 Class 2 mutation in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene.  Dorsal, ventral and lateral lobes only.


title: Ms3888_5ul_CRE_36h_NoED_Rep1

value: 3888 (Del+/+; Trp53f/f)  prostate organoid

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: HRCRC3869_RNA-seq

value: IIA


title: Namalwa-control 2

value: lymphpblast

value: Namalwa

value: B lymphpblast

value: WT


title: Ms#3650_R265-71del+/+; Trp53f/f PbCre+_AD_Case_Lib1

value: mixed


title: Namalwa-XMU-0.3-2

value: XMU-MP-1 0.3 µM


title: Ms2114_P358fs_A_CRE_NoED_Rep1

value: prostate

value: 2114 (P358fs+/-) prostate organoid


title: Ms2114_P358fs_A_CRE_NoED_Rep2

value: male


title: Ms#3652_R265-71del+/+; Trp53f/f PbCre+_AD_Case

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre+ mice have expression of the transgene.Anterior and Dorsal lobes only from 100-week old animals


title: HRCRC3814_RNA-seq

value: Non-mucinous adenocarcinoma

value: non-mucinous colorectal cancer tissue


title: HRCRC3847_RNA-seq

value: IIIB


title: Namalwa-control 1


title: TI1_008

city: Leiden

first: Robert

last: Kleemann

address: Sylviusweg 71

country: Netherlands

institute: The Netherlands Organisation for Applied Scientific Research

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Homo_sapiens.GRCh38.gencode.v29
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: primary cell line

growth_protocol: Cryopreserved primary healthy human HSCs (iXCells Biotechnologies, Lot#PFP, #25914) were thawed and plated for expansion in Poly-L-Lysine (PLL) (2 μg/cm2) (ScienceCell Research Laboratories) 75 cm2 coated flasks (Greiner, Cat#658175) to enhance cell attachment. Primary HSCs were seeded in Stellate cell medium (SteCM) containing 2% FBS 1%, penicillin/streptomycin (PS) and 1% Stellate cell growth supplement (SteCGS) (ScienceCell, SCC5301). Cells were incubated at 37°C and 5% CO2.  After 4h, when cells were attached to the bottom of the flask, they were refreshed with new SteCM medium. Cells were passaged after 7 days of culture by detaching them with 2.5 ml/flask accutase (Sigma, Cat#A6964). After 3-5 min incubation, accutase was inactivated with 7.5 ml/flask SteCM medium. Cells were counted with Scepter™ 3.0 Cell Counter with 60 μm counter sensors and seeded in 24-well cell culture plates (Costar Corning, Cat#3524) coated with fibronectin (Merck Life Science #10838039001) at a density of 3.69E+04 cells/well in a final volume of 500 μl/well.

extract_protocol:
Next generation sequencing (NGS) was performed in RNA samples extracted from the 8 conditions mentioned above in biological duplicates. RNA was isolated using the RNAqeus Microkit (Thermo Fisher Scientific, Cat#AM1931) and RNA concentrations were determined using NanoDrop 2000 (Unigen Life Sciences) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-77 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: The following day (day 1), before trigger solutions were added, cells were washed with SteCM containing 1% FBS and 1% PS. Trigger solutions were prepared in complete SteCM containing 1% FBS, 1% PS, 1% insulin-transferrin-sodium selenite (ITS) (Sigma, Cat#I3146), 173 μM ascorbic acid (AA) (Sigma, Cat#A8960), 2.5 mM L-proline (Sigma, P5607), 2.5 mM lysine (Sigma, Cat#62840), and 2.5 mM glycine (Sigma, Cat#G5417). Trigger solutions included combinations of TGF-β1 (R&D Systems, Cat#240-B) at a concentration of 4 ng/ml, Alk5 inhibitor (Millipore #616459) at a concentration of 5 μM and IOX2 (Sigma, Cat#SML0652) at concentrations of 0.3 μM and 1 μM.  In total, 8 different trigger solutions (control, IOX2 0.3, IOX2 1, TGF-β1, TGF-β1 + Alk5, TGF-β1 + IOX2 0.3, TGF-β1 + IOX2 0.3 + Alk5 and TGF-β1 + IOX2 1) were added in a final volume of 300 μl/well and incubated for 4 days.

value: primary cell line

value: Healthy LiverStellate Cells

value: iXCells Biotechnologies, Lot#PFP, #25914.


title: TI1_016


title: Ms2114_P358fs_A_control_NoED_Rep2

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: TI.3A_015


title: HRCRC3796_RNA-seq

value: IIA


title: Emg1 conditional KO mutant caudal region of E10.5 embryos, rep3

city: Izumi

first: Isao

last: Matsuo

state: Osaka

address: 840 Murodo-cho

department: Department of Molecular Embryology

country: Japan

institute: Research Institute, Osaka Women's and Children's Hospital,  Osaka Prefectural Hospital Organization

data_processing:
The sequencing reads were trimmed using Trimmomatic v0.39
Trimmed  reads were aligned to the mm10 genome assembly using STAR v2.7.10b
Read count extraction and normalization were performed using StrandNGS v4.0
Assembly: mm10
Supplementary files format and content: excel spreadsheet file includes raw counts and TPM values for each Sample

source_name: caudal embryonic region

extract_protocol:
Total RNA was extracted from the caudal region of mouse embryos using miRNeasy mini kit (Qiagen).
RNA library for RNA-Seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacture’s protocols.

value: caudal embryonic region

value: Emg1 cKO


title: Namalwa-XMU-2.5-1

value: lymphpblast

value: Namalwa

value: B lymphpblast

value: WT

value: XMU-MP-1 2.5 µM


title: TI.3A_007


title: Ms1947_P358fs_C_CRE_NoED_Rep2

value: prostate

value: 1947 (P358fs+/-) prostate organoid

value: mixed

value: male


title: Ms#3651_3646_R265-71del+/+; Trp53f/f PbCre-_AD_Ctrl

value: R265-71del+/+; Trp53f/f PbCre-

value: Mice with conditional overexpression of the FOXA1 Class 1 mutation and loss of Trp53 in the prostate epithelial cells. Pb-Cre- mice have no expression of the transgene. Anterior and Dorsal lobes only from 100-week old animals


title: Ms1947_P358fs_C_CRE_NoED_Rep1


title: Emg1 conditional KO mutant caudal region of E10.5 embryos, rep2


title: HRCRC3864_RNA-seq

value: Non-mucinous adenocarcinoma

value: female

value: non-mucinous colorectal cancer tissue


title: TI.3_014

value: primary cell line

value: Healthy LiverStellate Cells

value: iXCells Biotechnologies, Lot#PFP, #25914.


title: HRCRC3759_RNA-seq

value: I


title: Ms1947_P358fs_C_control_NoED_Rep2

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: HRCRC3745_RNA-seq

value: IIB


title: Vangl2 Lp/Lp mutant caudal region of E10.5 embryos, rep3

value: caudal embryonic region

value: Vangl2 Lp/Lp


title: Ms1947_P358fs_C_control_NoED_Rep1

value: prostate


title: Emg1 conditional KO mutant caudal region of E10.5 embryos, rep1

value: Emg1 cKO


title: TI.3_006


title: TA_013

value: TA


title: Ms2114_P358fs_A_control_NoED_Rep1

value: 2114 (P358fs+/-) prostate organoid

value: mixed

value: male


title: HRCRC3620_RNA-seq

value: Non-mucinous adenocarcinoma

value: IIA


title: HRCRC3615_RNA-seq

value: IV

value: non-mucinous colorectal cancer tissue


title: Vangl2 Lp/Lp mutant caudal region of E10.5 embryos, rep2


title: Ms1936_Class_3_CRE_NoED_Rep2

value: 1936 (FOXA1 WT+/-) prostate organoid

value: (FOXA1 WT+/-+, Cre+)


title: Ms1936_Class_3_CRE_NoED_Rep1


title: Vangl2 Lp/Lp mutant caudal region of E10.5 embryos, rep1


title: HRCRC3555_RNA-seq

value: female

value: I


title: T_012

value: primary cell line

value: Healthy LiverStellate Cells

value: iXCells Biotechnologies, Lot#PFP, #25914.

value: T


title: HRCRC3537_RNA-seq

value: IIIB


title: TA_005

value: TA


title: Ms1936_Class_3_control_NoED_Rep2

value: prostate

value: (FOXA1 WT+/-, Cre-)

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: beta-catenin conditional KO mutant caudal region of E10.5 embryos, rep3

value: caudal embryonic region

value: beta-catenin cKO


title: HRCRC3522_RNA-seq

value: Non-mucinous adenocarcinoma

value: male

value: IIIC


title: Ms1936_Class_3_control_NoED_Rep1

value: 1936 (FOXA1 WT+/-) prostate organoid

value: mixed


title: beta-catenin conditional KO mutant caudal region of E10.5 embryos, rep2


title: T_004


title: beta-catenin conditional KO mutant caudal region of E10.5 embryos, rep1


title: I1_011


title: I1_003


title: Ms1706_R261G_CRE_NoED_Rep1

value: 1706 (R261G+/+) prostate organoid


title: HRCRC3517_RNA-seq

value: non-mucinous colorectal cancer tissue


title: wild type control caudal region of E10.5 embryos, rep3

value: wild type


title: Ms1706_R261G_CRE_NoED__Rep2


title: Ms1706_R261G_control_NoED_Rep2


title: I.3_010

value: primary cell line

value: Healthy LiverStellate Cells

value: iXCells Biotechnologies, Lot#PFP, #25914.


title: wild type control caudal region of E10.5 embryos, rep2


title: I.3_002


title: C_009

value: C


title: Ms1706_R261G_control_NoED_Rep1

value: prostate


title: HRCRC3457_RNA-seq

value: IIIB


title: HRCRC3450_RNA-seq

value: IIA


title: brain, female 6, sh-Angptl2

city: Montréal

first: Pauline

last: Mury

state: QC

address: 5000 rue Bélanger

country: Canada

institute: Montreal Heart Institute

description: 10X Genomics

data_processing:
Fastq files were processed using CellRanger (10X Genomics, version 7.0.1) to decompose cell barcodes and align cDNA sequences against the human genomic reference (hg19) provided by 10X Genomics
Assembly: mm10
Supplementary files format and content: hdf5 file containing counts, and metadata on the rows (genes) and columns (cells)

source_name: brain

extract_protocol:
Mice were sacrificed using 3% isoflurane followed by exsanguination. Brain were then harvested, hypocampus isolated and snap frozen within 15min and stored at -80oC. Fifty miligrams of hypocampus were processed using GentleMACS Octo Dissociator and its nuclei lysis buffer, according the the manufacturer's instructions. Nuclei were then washed, filtered (100 and 70µm + 20 µm stack together) and resuspended in PBS-BSA 0.1%.
Libraries were prepared using the Next GEM Single Cell 3' Dual Indexing kit (10X Genomics) using a Chromium Controller instrument to generate single-nuclei gel bead-in-emulsion (GEMs). Then, GEMs were reverse transcribed into cDNAs that were then amplified and cleaned up using SPRIselect Reagent Kit (Beckman Coulter). The barcoded sequencing libraries were constructed by enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

treatment_protocol: Mice were treated with the virus at 6 months old and 7 and a half months old before sacrifice at 9 months old.

value: brain


title: C_001


title: HRCRC3419_RNA-seq


title: brain, male 5, sh-SCR

description: 10X Genomics

value: scramble


title: ITA, woman 6, quercetin

description: 10X Genomics

data_processing:
Fastq files were processed using CellRanger (10X Genomics, version 7.0.1) to decompose cell barcodes and align cDNA sequences against the human genomic reference (hg19) provided by 10X Genomics
Assembly: hg19
Supplementary files format and content: hdf5 file containing counts, and metadata on the rows (genes) and columns (cells)

source_name: thoracic artery

extract_protocol:
Thoracic arteries were harvested in operating room and snap frozen within 15min and stored at -80oC. Frozen segments were processed using GentleMACS Octo Dissociator and its nuclei lysis buffer, according the the manufacturer's instructions. Nuclei were then washed, filtered (70µm and 20µm) and resuspended in PBS-BSA 0.1%.
Libraries were prepared using the Next GEM Single Cell 3' Dual Indexing kit (10X Genomics) using a Chromium Controller instrument to generate single-nuclei gel bead-in-emulsion (GEMs). Then, GEMs were reverse transcribed into cDNAs that were then amplified and cleaned up using SPRIselect Reagent Kit (Beckman Coulter). The barcoded sequencing libraries were constructed by enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

treatment_protocol: Patients received randomly quercetin or placebo 500mg twice a day for 2 days before the surgery

value: thoracic artery

value: quercetin


title: HRCRC3503_RNA-seq

value: Non-mucinous adenocarcinoma

value: male

value: IIIC


title: ITA, man 6, placebo

description: 10X Genomics

value: placebo


title: HRCRC3348_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: Ms1218_sgNC_Rep2

value: 1218 (R261G+/-) prostate organoid

value: mixed

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: brain, female 5, sh-SCR

description: 10X Genomics


title: Ms1218_sgNC_Rep1


title: HRCRC3483_RNA-seq


title: wild type control caudal region of E10.5 embryos, rep1

value: caudal embryonic region

value: wild type


title: ITA, woman 5, placebo

description: 10X Genomics


title: HRCRC3337_RNA-seq

value: IV


title: brain, female 4, sh-Angptl2

description: 10X Genomics


title: HRCRC3328_RNA-seq

value: IIIB


title: brain, female 3, sh-SCR

description: 10X Genomics

value: brain


title: ITA, man 5, quercetin

description: 10X Genomics


title: Ms1218_sgNC_No_EGF_DHT_Rep1

value: prostate


title: Ms1218_sgTrp53_Rep2

value: 1218 (R261G+/-); Trp53 knock-out prostate organoid

value: (R261G+/-, Cre-; Trp53 knock-out)


title: Ms1218_sgTrp53_Rep1


title: ITA, woman 4, quercetin

description: 10X Genomics

value: thoracic artery

value: quercetin


title: HRCRC3295_RNA-seq

value: Non-mucinous adenocarcinoma


title: HRCRC3351_RNA-seq

value: male

value: IIA


title: brain, male 6, sh-Angptl2

description: 10X Genomics


title: brain, male 4, sh-Angptl2

description: 10X Genomics


title: Ms1218_sgNC_24h_10nM_DHT_Rep2

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.  Organoids were then stimualted with 10nM DHT for 24 hours


title: brain, male 3, sh-SCR

description: 10X Genomics

value: scramble


title: HRCRC3275_RNA-seq

value: female

value: I

value: non-mucinous colorectal cancer tissue


title: ITA, woman 3, placebo

description: 10X Genomics

value: placebo


title: HRCRC3291_RNA-seq

value: IIB


title: brain, female 2, sh-SCR

description: 10X Genomics


title: Ms1218_sgNC_No_EGF_DHT_Rep2

value: 1218 (R261G+/-) prostate organoid

value: mixed

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.


title: Ms1218_CRE_sgNC_No_EGF_DHT_Rep2

value: prostate


title: Ms1218_CRE_sgNC_No_EGF_DHT_Rep1


title: HRCRC3242_RNA-seq


title: HRCRC3221_RNA-seq


title: ITA, woman 2, quercetin

description: 10X Genomics


title: brain, male 2, sh-Angptl2

description: 10X Genomics

value: brain


title: brain, female 1, sh-Angptl2

description: 10X Genomics


title: ITA, man 2, quercetin

description: 10X Genomics

value: thoracic artery


title: HRCRC3197_RNA-seq

value: IV


title: Ms1947_CRE_CST

value: 2114 (P358fs+/-) prostate organoid

value: Cre+ virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Mutant Foxa1 ChIP-seq was performed.


title: ITA, woman 1, placebo

description: 10X Genomics


title: Ms1947_Control_TFS

value: male

value: Cre- virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Wild-type FOXA1 ChIP-seq was performed.


title: Ms1218_sgNC_24h_10nM_DHT_Rep1

value: Prostate organoids were seeded at a density of 20,000 cells/40ul matrigel dome in 2 replicates on Day 0 and incubated for 48 hours in the complete organoid media, followed by a 12-hour starvation in media lacking EGF and DHT.  Organoids were then stimualted with 10nM DHT for 24 hours


title: brain, male 1, sh-SCR

description: 10X Genomics

value: scramble


title: HRCRC3957_RNA-seq

value: Non-mucinous adenocarcinoma

value: female

value: IIIC


title: ITA, man 4, placebo

description: 10X Genomics

value: placebo


title: Sample_9_KI

city: Bonn

first: Rayk

last: Behrendt

address: Venusberg-Campus 1

department: Institute for Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Bonn

data_processing:
Count files (fastq) were preprocessed for quality and adapter trimming using cutadapt (v.4.9) (DOI: https://doi.org/10.14806/ej.17.1.200). High quality reads were aligned using Salmon (v1.7) to the mm10 transcriptome (GCA_000001635.2) and checked for quality using Fastqc (v.0.12.0) and Multiqc (v1.11).
Differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Biological outliers (1 wild-type and 2 IFNa4-KI samples) were determined using PCA and heatmap visualization and removed for final analysis. Two sequencing runs were conducted and raw data was batch corrected using CombatSeq in sva package (v.3.38.0)
Comparisons were run using LRT test and multiple testing correction was implemented using the Benjamini Hochberg method. The cutoff for differentially expressed genes (DEGs) was Padj < 0.05. Heatmaps were visualized using the pheatmap package (v.1.0.12)
Assembly: mm10
Supplementary files format and content: tar zip file of salmon outputs including plaint text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

source_name: Spleen

extract_protocol:
Total RNA was isolated from whole spleen with Trizol according to manufacture’s protocol (Thermo Fisher) followed by DNAse treatment.
cDNA libraries libraries were prepared at the Next Generation Sequencing Core Facility of the Medical Faculty/West German Genome Center Bonn at the University of Bonn using the QuantSeq 3´-mRNA Library protocol from Lexogen.
Sequencing was performed on an Illumina NovaSeq 6000 platform to generate 1x100bp reads resulting in an average depth of 10 million Raw Reads per sample.

value: Spleen


title: HRCRC3936_RNA-seq

value: non-mucinous colorectal cancer tissue


title: Sample_8_KI


title: Ms2114_CRE_CST

value: mixed

value: Cre+ virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Mutant FOXA1 ChIP-seq was performed.


title: ITA, man 1, quercetin

description: 10X Genomics

value: quercetin


title: HepG2 control cells, bio rep 3

city: Shenzhen

first: jianhua

last: zhong

address: 3025 Shennan Road Central, Futian District, Shenzhen

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

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads 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 selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg19
Supplementary files format and content: the file includes raw counts for each Sample

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

value: HepG2 cells transfected with pmCherry-N1 (control) plasmid.


title: ITA, man 3, placebo

description: 10X Genomics

value: thoracic artery


title: Ms2114_CRE_KLF5

value: prostate

value: 2114 (P358fs+/-) prostate organoid

value: Cre+ virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Klf5 ChIP-seq was performed.


title: Sample_7_KI


title: HRCRC3932_RNA-seq

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.7.3a).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were assessed using the RNA Integrity Number (RIN).
TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA)

value: IV


title: HRCRC3927_RNA-seq

value: male

value: IIA


title: Sample_6_KI


title: Ms2114_Control_TSF

value: Cre- virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Wild-type FOXA1 ChIP-seq was performed.


title: HepG2 control cells, bio rep 1


title: HRCRC3904_RNA-seq

value: Non-mucinous adenocarcinoma


title: Ms1706_CRE_AR

value: 1706 (R261G+/+) prostate organoid

value: Cre+ virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Ar ChIP-seq was performed


title: Ms2114_Control_KLF5

value: Cre- virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Klf5 ChIP-seq was performed.


title: Sample_5_WT

value: Spleen

value: WT


title: HepG2-HBx cells, bio rep 3

value: HepG2 cells transfected with HBx plasmid


title: HRCRC3900_RNA-seq

value: IIB

value: non-mucinous colorectal cancer tissue


title: Ms1706_Control_AR

value: mixed

value: Cre- virus treated-organoids were grown in complete mouse prostate media for 48 hours followed by a 6hour incubation with 1nM R1881 prior to harvest. Ar ChIP-seq was performed


title: HRCRC3898_RNA-seq

value: female

value: IIIB


title: Sample_4_WT


title: HepG2-HBx cells, bio rep 2


title: Mouse cortex shFabp7-LPS-3

city: Madison

first: Marcelo

last: Vargas

state: WI

address: 600 Highland Avenue

institute: UW-Madison

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed sequence reads were mapped to GRCm39 using the STAR aligner v.2.5.2b
Read count extraction was performed using Subread Package v.1.5.2 and differential gene expression analysis was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: Cerebral cortex

extract_protocol:
RNA was harvested using TriReagent. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep.

treatment_protocol: At 21 days of age mice received a retro-orbital injection of an AAV-PHPeB vector (5x1013vg/kg ) that codes for an embedded non-silencing scramble (AAV-PHP.eB-Gfap-GFP-shScr) or a Fabp7-specific shRNA (AAV-PHP.eB-Gfap-GFP-shFABP7) under the control of a Gfap promoter. At 4 months of age, animals were injected with LPS (1mg/kg) once a week for 3 consecutive weeks and harvested 24h after the last injection.

value: Cerebral cortex

value: wild type

tag: viral treatment

tag: time

value: 24h-post last injection


title: HepG2 control cells, bio rep 2

value: HepG2 cells transfected with pmCherry-N1 (control) plasmid.


title: Spheroids #5 - Decidualized infected

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

data_processing:
Analysis with megSAP pipeline (https://github.com/imgag/megSAP)
Adaptor removal with SeqPurge (ngs-bits)
Read to genome alignment with STAR
Alignment deduplication based on UMI with umi_tools
Gene read counting with featureCounts (subread)
Assembly: GRCh38
Supplementary files format and content: gene read counts in tabular format

source_name: Ishikawa/HESC

growth_protocol: A well differentiated endometrial carcinoma cell line (Ishikawa cells, ECACC #99040201, Sigma Aldrich) and endometrial stromal cells were cultured togther in a humidified atmosphere of 5% CO2 at 37 ºC in Dulbecco’s modified Eagle’s medium F-12 (DMEM: F12) phenol free supplemented with 10% (v/v) FBS, 1% antibiotic/antimycotic solution and 0.25% L-Glutamine (Invitrogen, Germany), which was replenished every 48h.  Spheriods were passaged when the confluency reached at 80%. When performing experiments, cells were cultured in DMEM: F12 phenol free supplemented with 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution overnight. .

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA kit with poly(A)+ selection

treatment_protocol: Endometrial spheroids were cultured in agarose-coated 96-well plates for seven days and treated with decidualization medium for five days prior to infection. Spheroids were infected with SARS-CoV-2 B.1.617.2 (isolated from a throat swab collected in May 2021 at the Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen [28])at an MOI of X. After 48 h of incubation at 37°C, spheroids were collected (12 spheroids per sample), washed with PBS and prepared for RNA isolation.

value: Ishikawa/HESC

value: epithelial/stroma

value: infected


title: HRCRC3849_RNA-seq

value: Non-mucinous adenocarcinoma

value: IIA


title: HRCRC3839_RNA-seq

value: male

value: IV


title: Sample_3_WT

value: Spleen

value: WT


title: HepG2-HBx cells, bio rep 1

value: HepG2 cells transfected with HBx plasmid


title: Spheroids #5 - Control infected


title: Mouse cortex shFabp7-LPS-2

value: LPS (1mg/kg) once a week for 3 consecutive weeks


title: Sample_2_WT


title: HRCRC3823_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: Sample_8_KI_anti_IFNAR1

data_processing:
Count files (fastq) were preprocessed for quality and adapter trimming using cutadapt (v.4.9) (DOI: https://doi.org/10.14806/ej.17.1.200). High quality reads were aligned using Salmon (v1.7) to the mm10 transcriptome (GCA_000001635.2) and checked for quality using Fastqc (v.0.12.0) and Multiqc (v1.11).
Differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Biological outliers (1 wild-type and 2 IFNa4-KI samples) were determined using PCA and heatmap visualization and removed for final analysis. Two sequencing runs were conducted and raw data was batch corrected using CombatSeq in sva package (v.3.38.0)
Comparisons were run using LRT  test and multiple testing correction was implemented using the Benjamini Hochberg method. The cutoff for differentially expressed genes (DEGs) was Padj < 0.05. Heatmaps were visualized using the pheatmap package (v.1.0.12)
Assembly: mm10
Supplementary files format and content: tar zip file of salmon outputs including plaint text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters


title: Mouse cortex shScr-LPS-3

value: Cerebral cortex


title: Sample_1_WT


title: Sample_7_KI_anti_IFNAR1


title: HRCRC3809_RNA-seq

value: IIIB


title: Mouse cortex shFabp7-LPS-1

value: wild type

value: 24h-post last injection


title: Mouse cortex shScr-LPS-2


title: Spheroids #5 - Control non-infected

value: Ishikawa/HESC

value: non-infected


title: HRCRC3807_RNA-seq

value: IIIC


title: Spheroids #4 - Decidualized infected

value: epithelial/stroma

value: infected


title: Mouse cortex shScr-LPS-1


title: Sample_6_KI_anti_IFNAR1


title: HRCRC3752_RNA-seq

value: Non-mucinous adenocarcinoma

value: male

value: IIA


title: Sample_5_KI_anti_IFNAR1

value: Spleen


title: HRCRC3744_RNA-seq


title: BMDM, 24h, RRP1,RIP,replicate2

city: Suzhou

first: Zhou

last: Yumei

address: No.100,Chongwen Road

institute: Suzhou Institute of Systems Medicine,Chinese Academy of Medical Sciences

library_source: other

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
RIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Seqtk v1.0-r82-dirty, discarding reads left with < 20 bp
RIP-seq reads were aligned to the ensembl mm10 genome using Tophat2 version 2.1.0. Only uniquely mapping reads with at most two mismatches were retained.
To create RIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to FPKM)
Peaks were called using RIPSeeker with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include peak values for each Sample

molecule: other

source_name: bone marrow

growth_protocol: Bone marrow was harvested from C57BL/6 mice and cultured in DMEM medium supplemented with 25 ng ml−1 murine M-CSF, 10% FBS, and 1 Penicillin-Streptomycin.The cells were cultured for 7 days with fresh media changed every other day

extract_protocol:
Cells were harvested using RIP lysis buffer. A primary antibody that recognized RRP1 or control IgG was added to the supernatants overnight at 4°C. Protein A/G Magnetic Beads were then added and gently mixed for 1 h at 4°C. The beads were washed with NT2 buffer 5 times before digestion with Proteinase K in buffer for 30 min at 55°C to remove proteins. The RNA was isolated using TRIzol LS and further assessed by high-throughput sequencing.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using randomhexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. Endreparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCRamplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: Cells were treated with 50 ng/mL IL-1β for the indicated hous.

value: bone marrow

value: bone marrow derived macrophages

value: macrophages

value: wilde tye

value: IL-1B stimulated for 24 hours


title: Sample_4_KI_IgG


title: HRCRC3731_RNA-seq

value: female

value: non-mucinous colorectal cancer tissue


title: BMDM, 24h, RRP1,RIP,replicate1


title: Spheroids #4 - Decidualized non-infected


title: BMDM, 12h, RRP1,RIP,replicate2

value: IL-1B stimulated for 12 hours


title: BMDM, 12h, RRP1,RIP,replicate3


title: HRCRC3677_RNA-seq

value: IV


title: Spheroids #1 - Decidualized infected

value: Ishikawa/HESC


title: Spheroids #5 - Decidualized non-infected

value: non-infected


title: Sample_2_KI_IgG


title: Sample_3_KI_IgG


title: HRCRC3571_RNA-seq

value: IIIC


title: Spheroids #4 - Control non-infected

value: epithelial/stroma


title: BMDM, 12h, RRP1,RIP,replicate1


title: Sample_1_KI_IgG


title: HRCRC3601_RNA-seq

value: Non-mucinous adenocarcinoma

value: IIB


title: Spheroids #1 - Decidualized non-infected


title: Spheroids #1 - Control non-infected


title: TLR9_KO_M_Flu3

city: NEW HAVEN

first: Yifan

last: Yuan

state: CT

address: 10 Amistad st, 314

institute: yale university school of medicine

description: 10x Genomics

data_processing:
RNA-Seq Data Filtration, Normalization, Scaling, Integration, and Clustering: Aligned data was processed using Seurat v3.1.2 under R environment. Default parameters were used for each function unless otherwise specified. After creating Seurat objects for each sample, we filtered on the percent mitochondrial genes to exclude damaged and dying cells and on the number of genes and transcripts to remove debris and doublets. All samples after filtration were integrated by the IntegrateData function in Seurat. The gene counts in the integrated object were then normalized to the total counts and multiplied by a 10,000 scaling factor. We used Variance Stabilizing Transformation (VST) to select highly variable genes. The top 200 genes within the selected genes were retained for downstream analysis. Variable genes were scaled using Seurat’s ScaleData function and subsequently were used for principal component analysis (PCA) to generate clusters. The numbers of clusters produced using PCA analysis are controlled by a resolution parameter with higher values giving more clusters and by the number of PCs. All cells across different samples were assigned into two-dimensional Uniform Manifold Approximation and Projection (UMAPs).
Assembly: GRCm38.p6(GCA_000001635.8)
Supplementary files format and content: barcodes.tsv.gz; matrix.mtx.gz; features.tsv.gz; CellRanger processed data

source_name: Lung

growth_protocol: Lung samples from WT and TLR9-/- animals were obtained on day 4 post-infection to determine cell-specific differences in early infection and antiviral responses.

extract_protocol:
Lung samples across different conditions were digested with collagenase type 4 (2mg/ml) and DNase (20U/ml) in DMEM with 10% FBS to prepare single-cell suspension for an expected cell recovery population of 10,000 cells per lane.
scRNAseq libraries were generated with the Chromium Single Cell 3’ assay (10x Genomics) and were sequenced on the NovaSeq platform per library in Yale Center for Genomics Analysis. Downstream processing was conducted with Cellranger 3.0.2 with the default parameters.

treatment_protocol: No treatment was provided other than the infection or mock infection (with PBS) under ketamine/xylazine anesthesia.

value: Lung

value: Flu


title: BMDM, 24h, RRP1,RIP,replicate3

value: bone marrow


title: BMDM, 0h, RRP1,RIP,replicate3

value: bone marrow derived macrophages

value: no IL-1B stimulated


title: Spheroids #4 - Control infected

value: infected


title: TLR9_KO_F_Flu1

description: 10x Genomics


title: HRCRC3470_RNA-seq

value: male


title: AD bcmap rep 2

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

data_processing:
Barcodes were mapped to the barcode map processed file to construct a barcode count matrix
Assembly: hg19
Supplementary files format and content: AD_MPRA_countTable.txt; barcode counts across all samples and their respective variant to be used for downstream processing, AD_MPRA_Barcode_Map.txt; barcode to variant mapping
Library strategy: MPRA

source_name: plasmid

growth_protocol: THP-1 monocytes were cultured in RPMI 1640 media with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated from resting and treated macrophages and reverse transcribed into cDNA. cDNA was amplified with GFP primers to select for barcodes.
Modified MPRA library preparation

treatment_protocol: THP-1 monocytes were transduced with lenti-MPRA and grown for 5 days before being differentiated into macrophages by treatingw ith 25 µM PMA for 24h. After 72h rest, macrophages were treated with 10 ng/mL of LPS and  20 ng/mL INFγ for 24h to induce a proinflammatory state.

value: plasmid


title: Spheroids #1 - Control infected


title: AD bcmap rep 1


title: HRCRC3426_RNA-seq

first: Jeewoo

last: Seo

institute: Korea Research Institute of Bioscience and Biotechnology, KRIBB

value: female

value: non-mucinous colorectal cancer tissue


title: HRCRC3423_RNA-seq

value: IIIB


title: BMDM, 0h, RRP1,RIP,replicate1

value: Primary bone marrow derived macrophages

value: macrophages

value: wilde tye


title: HRCRC3424_RNA-seq

value: IIA


title: WT_M_Flu2

description: 10x Genomics

value: Wildtype


title: HRCRC3391_RNA-seq

value: Non-mucinous adenocarcinoma


title: RNA-seq_cKO_rep2

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
For CLIP-seq, UMIs were first trimmed and added to the name of read names. After removing adaptor sequences, CLIP-seq reads longer than 18nt were mapped to the reference mouse genome (mm10) with Bowtie. Duplicated reads were collapsed based on both UMIs and mapping positions.
For RNA-seq, paired-end clean reads were aligned to this reference genome using HISAT2 software (version 2.0.5). FeatureCounts (version 1.5.0) was then employed to enumerate reads mapped to each gene. Following this, an FPKM value of each gene was calculated, factoring in both the gene's length and the read count mapped to it. Differential gene expression between Bcas2-cKO and control mice (comprising a biological replicate per condition) were conducted using the DESeq2 R package (version 1.20.0). Genes demonstrating a padj value ≤0.05, as identified by DESeq2, were delineated as differentially expressed.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, the 100000000 isolated B cells were irradiated at 400mJ/cm2 with 254nm UV light. The crosslinked cells were lysed and 15ug of BCAS2 (Abmart, Catalog # PA2466S) specific antibody was applied to pull-down protein-RNA complexes. After micrococcal nuclease treatment, 3’RNA linker ligation and 5’end 32P labeling, the immunoprecipitated complexes were fractionated on 10% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The auto-radiographed BCAS2 smear bands were cut and treated with Proteinase K to extract respective RNA by phenol and chloroform. The isolated RNA was then added a 5’ RNA linker and reverse transcribed by superscript reverse transcriptase III (life technologies, catalog# 18080-051). The PCR products were sequenced with illumina Hiseq 2500 platform. RNA-seq was performed as follows. mRNA from B cells was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, a transcriptome sequencing library was established. Utilizing a TruSeq PE Cluster kit v3-cBot-HS (Illumina) on a cBot Cluster Generation System, index-coded samples were clustered in strict accordance with the manufacturer’s guidelines. Upon completion of the clustering process, the library preparations were subjected to sequencing on the Illumina NovaSeq platform, generating 150 bp paired-end reads. Rigorous quality control measures were implemented post-sequencing to ensure that downstream analyses were performed exclusively on pristine, high-quality data.

value: Spleen

tag: strain

value: B cells

value: Bcas2 KO

value: LPS+IL4 treatment

tag: antibody

value: No antibody


title: RNA-seq_CTRL_rep2

value: Wild type


title: HRCRC3561_RNA-seq

value: male


title: Lenti DNA seq rep 1

source_name: lentiviral construct

value: lentiviral construct


title: HRCRC3326_RNA-seq

value: female

value: IV


title: RNA-seq_CTRL_rep1