title: Patient 10, PARCB transformed endpoint tumor cells, 8.5wks

city: Los Angeles

first: Owen

last: Witte

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

data_processing:
TOIL pipeline v 3.12.0 (http://toil.ucsc-cgl.org/)
Sequence reads were trimmed for adaptor sequences/low-quality sequences using CutAdapt and FastQC from TOIL pipeline
Trimmed sequence reads were mapped to hg38 human genome using STAR from TOIL pipeline
Expected read counts were quantified using RSEM from TOIL pipeline
Upper quartile normalization and log transformation were performed on expected read counts
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains log2(upper quartile normalized counts + 1) for each sample

source_name: Prostate

extract_protocol:
Tumors were dissociated into single cells, followed by cell sorting of triple colors (RFP, GFP and YFP) by flow cytometry. Total RNA was extracted from the cell lysates using miRNeasy kit (Cat# 217084, Qiagen).
Libraries for RNA-Seq of PARCB time course samples were prepared with KAPA Stranded mRNA-Seq Kit (Cat# KK8420, Roche). The workflow consists of mRNA enrichment and fragmentation.

value: Prostate

value: Xenograft

tag: sample type

value: Endpoint Tumor

tag: tumor collection_time

value: PARCB transformation


title: Hippocampus WT at P1 1

status: Public on Nov 24 2023

type: SRA

city: Gifu

first: Kazuya

last: Tokumura

address: 1-25-4 Daigakunishi

department: Bioactive Molecules

country: Japan

institute: Gifu Pharmaceutical University

library_source: transcriptomic

data_processing:
Sequence reads were trimmed using Trimgalore version 0.6.6 to exclude low-quality bases.
Trimmed sequence reads were mapped to GRCm39/mm39 using STAR version 2.7.8a.
Gene expression levels were determined by measuring the number of reads mapped to each gene region using RSEM version 1.3.3.
Assembly: mm39
Supplementary files format and content: tab-delimited text file raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

growth_protocol: Mice with one day of life were sacrificed by decapitation and the tissues (testes or hippocampus) were dissecated and freeze immediately in liquid nitrogen for porterior RNA isolation

extract_protocol:
RNA was harvasted using the Rneasy mini kit plus (Qiagen)
RNA libraries for RNA-seq were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina

tag: tissue

value: Hippocampus

tag: genotype

value: WT


title: SCD +AID_DCP2_replicate1_t40

city: Zürich

first: Mostafa

last: Zedan

address: Otto-Stern-Weg 3

country: Switzerland

institute: ETH-Zurich

data_processing:
The SLAM-DUNK software was used for reads alignment, filtration, calling SNP, and calculating the relevant statistics of SLAMSeq reads for each given 3’ UTR.
Assembly: The FASTA file of the Yeast Genome was downloaded from the Saccharomyces Genome Database "SGD"
Supplementary files format and content: A tab-separated tcount file per sample containing the SLAMSeq statistics

organism: Saccharomyces cerevisiae

extract_protocol:
Yeast cells were lysed and RNA was extracted using Phenol-Chlorform
Quantseq
3’mRNA-Seq

tag: cell line

tag: cell type

value: Yeast cells

tag: time after_chase

value: 40 min

tag: biological replicate

value: replicate 1

tag: treatment

value: plus Auxin and Estradiol


title: U123M15-T 6h culture No RX [mC1_6h]

city: Chicago

first: Qiaomu

last: Tian

address: 5841 S. Maryland Ave

country: USA

institute: University of Chicago

data_processing:
The reads were mapped to the Homosapien genome (GRCh38) using STAR software with ≥95% mapping rate.
Differential expression analysis was performed using DESeq2 package in R64
Molecular and cellular function analysis and pathway enrichment was analyzed using Ingenuine Pathway Analysis software (Qiagen).
Supplementary files format and content: GRCh38
Supplementary files format and content: read count, fpkm

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using a RNeasy® Plus Mini Kit (Qiagen), and total RNA quantified using the 2100 Bioanalyzer (Agilent).
Samples with a RIN >8 was outsourced to Novogene for library construction and sequencing (Illumina Platform (PE150)) with 20 M raw reads/sample.

treatment_protocol: Two organoids, U049MAI, U123M15-T, were cultured with CK21 at 50 nM for 3 hours, 6 hours, 9 hours and 12 hours.

value: Organoid

value: No Rx


title: Hippocampus WT at P1 3


title: SCD +AID_DCP2_replicate1_t35

value: 35 min


title: Testes Het at P1 1

source_name: Testes

value: Testes

value: Osteocalcin Heterozygous


title: U123M15-T 3h culture No RX [mC1_3h]


title: SCD +AID_DCP2_replicate1_t55

value: 55 min


title: Testes KO at P1 3

value: Osteocalcin KO


title: Testes Het at P1 2


title: Testes Het at P1 3


title: SCD +AID_DCP2_replicate1_t25

value: 25 min


title: Hippocampus KO at P1 2


title: Testes WT at P1 1


title: SCD +AID_DCP2_replicate1_t10

value: 10 min


title: KO_CVB3_7d_4

city: Freiburg

first: Diana

last: Lindner

address: Hugstetter Straße 55

department: University Heart Center Freiburg-Bad Krozingen

country: Germany

institute: University Hospital Freiburg

description: Sample 30

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto mm10 genome using bowtie2 and raw counts were obtained using HTSeq
Differential gene expression was calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: raw count and tpm count
Library strategy: Massive Analysis of cDNA ends (MACE-Seq)

source_name: Heart

extract_protocol:
Total RNA Isolation was performed using the miRNeasy mini kit (Qiagen, Germany). As suggested, DNase I (Qiagen, Germany) was applied to the column to avoid genomic DNA contamination.
Three prime End sequencing using GenXPro-MACE-Seq kit (GenXPro GmbH, Frankfurt Germany) including UMIs for PCR-dupliacate removal.

value: Heart


title: Patient 10, PARCB transformed early tumor cells, 4.5wks

state: California

molecule: polyA RNA

value: Prostate

value: Xenograft

value: Early Tumor

value: PARCB transformation


title: Testes KO at P1 2


title: SCD +AID_DCP2_replicate1_t20

value: Yeast cells

value: 20 min


title: KO_CVB3_7d_5

description: Sample 31


title: KO_CVB3_6d_5

description: Sample 28


title: Testes KO at P1 1


title: Patient 9, PARCB transformed transition tumor cells, 6wks

value: Transition Tumor


title: KO_CVB3_6d_4

description: Sample 27


title: SCD +AID_DCP2_replicate1_t5

value: 5 min

value: replicate 1

value: plus Auxin and Estradiol


title: Testes WT at P1 2

value: Testes

value: WT


title: SCD +AID_DCP2_replicate1_t15

value: 15 min


title: KO_CVB3_7d_2

description: Sample 25


title: Patient 10, PARCB transformed transition tumor cells, 6.5wks


title: SCD -AID_POP2/CCR4_replicate1_t55

value: 55 min

value: plus Ethanol


title: Patient 10, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: Patient 9, PARCB transformed endpoint tumor cells, 8wks

value: Prostate

value: Endpoint Tumor


title: Patient 10, PARCB transformed prostate organoid, 0wks

value: Prostate Organoid

value: Organoid


title: KO_CVB3_7d_3

description: Sample 29

value: Heart


title: SCD +AID_DCP2_replicate1_t30

value: Yeast cells

value: 30 min


title: KO_CVB3_6d_1

description: Sample 22


title: SCD -AID_POP2/CCR4_replicate1_t50

value: 50 min


title: KO_CVB3_6d_3

description: Sample 26


title: SCD +AID_DCP2_replicate1_t0

value: 0 min

value: replicate 1


title: KO_sh_6

description: Sample 21

value: sham


title: Patient 9, PARCB transformed prostate organoid, 0wks

value: PARCB transformation


title: SCD -AID_POP2/CCR4_replicate1_t45

value: 45 min


title: SCD -AID_POP2/CCR4_replicate1_t40

value: 40 min


title: Patient 9, PARCB transformed early tumor cells, 4wks

value: Xenograft

value: Early Tumor


title: KO_CVB3_7d_1

description: Sample 24


title: Patient 9, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: KO_sh_5

description: Sample 20


title: Patient 8, PARCB transformed transition tumor cells, 6wks

value: Prostate

value: Transition Tumor


title: KO_CVB3_6d_2

description: Sample 23


title: Patient 8, PARCB transformed endpoint tumor cells, 10wks

value: Endpoint Tumor


title: wt LAP* transdifferentiated cells

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Straße 10

department: Cell Differentiation and Tumorigenesis

institute: Max Delbrück Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
preprocessed by the Cellranger pipeline (version 2.1.0)
Analysis was done using Seurat 4 (Satija et al, 2015). Raw data was filtered, i.e.,cells with less than 400 features as well as more than 4000 features were removed. Additionally, cells containing a mitochondrial read percentage of more than 7 were removed as potentially dead cells. The WT and dKO samples were normalized using the 'LogNormalize' option, integrated and scaled. Dimension reduction by means of UMAP (McInnes et al, 2018) and clustering was performed by a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm with the resolution parameter set to 0.5.
Assembly: mm10
Supplementary files format and content: raw expression quantification in h5 format

source_name: B cells

growth_protocol: v-Abl-transformed pre-B cells were culture in completed DMEM medium (10%  fetal bovine serum(FBS), 10 mM HEPES and penicillin/streptomycin) supplemented with 50 mM beta-mercaptoethanol.

extract_protocol:
Cells at day 6 post-infection were subjected to EGFP sorting using AriaI/II/III (BD), EGFP positive cells were sorted directly into FACs buffer (HBSSwo, 2% FBS, 5mM EDTA) and further processed with single cell partitioning and scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

treatment_protocol: pMSCV_LAP*_3x-FLAG_IRES_EGFP vector was transfected into Plat-E packaging cells to generate infectious retroviral supernatant. Retroviral supernatant was added to B cells in 1:1 (V:V) ratio in complete DMEM supplemented with 50 mM beta-mercaptoethanol and 8 ug/mL polybrene. Cells were centrifuged at 2000 rpm without break at 37°C for 1 hour, following by overnight incubation.

value: B cells

value: mixed sample (Cebpa flox/flox, Cebpb flox/flox)

value: LAP* transdifferentiated


title: SCD -AID_POP2/CCR4_replicate1_t30

value: Yeast cells

value: 30 min

value: plus Ethanol


title: Patient 8, PARCB transformed transition tumor cells, 8wks


title: dko LAP* transdifferentiated cells

description: 10x Genomics

value: mixed sample (Cebpa -/-, Cebpb -/-)


title: KO_sh_4

description: Sample 19

value: Heart

value: sham


title: Patient 8, PARCB transformed early tumor cells, 4wks

value: PARCB transformation


title: KO_sh_1

description: Sample 16


title: SCD -AID_POP2/CCR4_replicate1_t35

value: 35 min

value: replicate 1


title: KO_sh_3

description: Sample 18


title: SCD -AID_POP2/CCR4_replicate1_t20

value: 20 min


title: Patient 8, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: KO_sh_2

description: Sample 17


title: WT_CVB3_6d_6

description: Sample 14

value: wildtype


title: Patient 8, PARCB transformed prostate organoid, 0wks

value: Prostate

value: Prostate Organoid

value: Organoid


title: SCD -AID_POP2/CCR4_replicate1_t15

value: 15 min


title: Patient 7, PARCB transformed endpoint tumor cells, 11wks

value: Xenograft

value: Endpoint Tumor


title: WT_CVB3_7d_3

description: Sample 15


title: WT_CVB3_6d_5

description: Sample 13


title: SCD -AID_POP2/CCR4_replicate1_t10

value: Yeast cells

value: 10 min

value: plus Ethanol


title: Patient 7, PARCB transformed transition tumor cells, 7wks

value: Transition Tumor


title: WT_CVB3_7d_2

description: Sample 12

value: Heart


title: SCD -AID_POP2/CCR4_replicate1_t5

value: 5 min


title: HET2_D30

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

description: gene expression (counts and normalized data)

data_processing:
We used FastQC for as first Quality Control step and MultiQC for summarization
Fastq files were processed using the Mappa (v1.0) pipeline from Takara (demuxer and analyser).
We ran demuxer to label the reads per cell, where the cell is included in the header of the sequence.
We ran the analyser, which includes read trimming with Cutadapt, Genome alignment with STAR and counting with Subread
Count summarization was done for exons only and for intron and exons.
Assembly: GRCh38
Supplementary files format and content: gene counts are given in csv format (Exons only SAMPLE_genematrix.csv, or also including introns SAMPLE_incl_introns_genematrix.csv)
Supplementary files format and content: normalized data for samples that come from whole cells and corresponding metadata are given in tsv format (TimeCourse_normalized_data.tsv and TimeCourse_metadata.tsv)

source_name: cell line

growth_protocol: KOLF2-C1 (HPSI0114i-kolf_2) and genome edited KOLF2-C1 derivatives were maintained on Matrigel-coated plates in Essential 8 media (TeSR-E8, Stemcell Technologies). All PSCs were passaged via manual dissociation using Gentle Cell Dissociation Reagent (Stemcell Technologies) as described previously (Arber et al 2015). IPSC differentiation towards mDA fate follows a protocol combining key features of (Kriks et al 2019) and (Jagger et al 2019). Briefly, PSCs were pre-plated on growth factor-reduced matrigel in TeSR-E8.  Neural differentiation was initiated when cells reached >80% confluence by switching to DMEM-F12/Neurobasal (2:1) supplemented with N2 and B27 (N2B27). For the first 7 days, cultures were supplemented with SB431542 (10µM, 1614-10 Tocris), LDN-193189 (100nM, StemGene), SHH-C24II (200ng/ml, 1845-SH-500 BioTechne) and Purmorphamine (1µM, 540220-5 VWR). LDN was kept until day 11. On day 3 CHIR99021 (3 µM, SM13-10 Cambridge Bioscience) was added to the media until day 13. Cultures were treated with PD0325901 from day 5 to 9 (1µM, SM26-10 Cambridge Bioscience).  FGF8a was added from day 11 to day 20 (100ng/ml, 100-25A Peprotech). Cultures were dissociated at around day 16/17 to single cells using Accutase (00-4555-56 Thermo Fisher Scientific) and replated onto poly-D-lysine/laminin coated plates at a density of 250000 cells/cm2. B27 without vitamin A (125870 Thermo Fisher Scientific) was used for the first 25 days, followed by B27 (175040 Thermo Fisher Scientific) plus BDNF (10ng/ml, 450-02-1MG Peprotech), GDNF (10ng/ml, GFH2-100 Cell Guidance System), Ascorbic Acid (200µM, A4544 Sigma-Aldrich) and DAPT (10µM, 2634 Tocris) from day 21 onwards.

extract_protocol:
We prepared single cell preparations from fresh cultures by incubation with Accutase 10 min at 37C followed by gently pipetting the cells 3-4 times and an extra 2 min incubation at 37C. After dissociation and pelleting, cells were pipetted to single cells in 500 ul PBS and incubated for staining with Hoechst and PI for 20 min at 37C (ReadyProbes™ Cell Viability Imaging Kit, Blue/Red, R37610 Invitrogen). After washing, we re-suspended the cells in 1ml PBS and filtered through a nylon membrane to remove cell clumps. We used Countess II Automated cell counter (Invitrogen) to quantify cell numbers and cells were dispensed at a concentration of 30.000 cells/ml into ICELL8 Single-Cell System (Takara).
The cDNA libraries were generated using the SMART-Seq ICELL8 cx Application Kit protocol provided by the manufacturer

value: cell line

value: KOLF2-C1 human iPSC line

value: iPSC differentiated into dopaminergic neurons

tag: clone

tag: differentiation day

tag: genetic modification

value: LMX1A Cre AAVS1 BFP

tag: type


title: Patient 7, PARCB transformed early tumor cells, 5wks

value: Early Tumor

value: PARCB transformation


title: HET2_D65


title: HET1_D30


title: HET1_D45

description: gene expression (counts)


title: HET1_D45_nuclei

molecule: nuclear RNA

value: nuclei


title: SCD -AID_POP2/CCR4_replicate1_t25

value: 25 min

value: replicate 1


title: WT_CVB3_7d_1

description: Sample 11

value: wildtype


title: WT_CVB3_6d_4

description: Sample 10


title: Patient 7, PARCB transformed transition tumor cells, 9wks

value: Prostate

value: Xenograft


title: SCD -AID_POP2/CCR4_replicate1_t0

value: Yeast cells

value: 0 min


title: SCD +AID_POP2/CCR4_replicate1_t50

value: 50 min

value: plus Auxin and Estradiol


title: Patient 7, PARCB transformed prostate organoid, 0wks

value: Prostate Organoid

value: Organoid


title: SCD +AID_POP2/CCR4_replicate1_t45

value: 45 min


title: SCD +AID_POP2/CCR4_replicate1_t55

value: 55 min


title: Patient 7, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: HET1_D21

value: cell line

value: KOLF2-C1 human iPSC line

value: iPSC differentiated into dopaminergic neurons

value: LMX1A Cre AAVS1 BFP


title: RKO cells, siANP32B-3

city: Shijiazhuang

first: Yinghao

last: Hao

state: Hebei

address: 215 Heping West Road

country: China

institute: The Second Hospital of Hebei Medical University

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GRCh38
Supplementary files format and content: Matrix table with FPKM and TPM values for each gene and each sample.

source_name: RKO

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: RKO

value: human colorectal cancer cell

value: ANP32B knockdown


title: WT_CVB3_6d_3

description: Sample 9

value: Heart

value: wildtype


title: WT_CVB3_6d_2

description: Sample 8


title: Patient 6, PARCB transformed endpoint tumor cells, 8wks

value: Prostate

value: Xenograft

value: Endpoint Tumor

value: PARCB transformation


title: WT_CVB3_6d_1

description: Sample 7


title: HET2_D21


title: RKO cells, siANP32B-2


title: RKO cells, siANP32B-1


title: WT_sh_6

description: Sample 6

value: sham


title: SCD +AID_POP2/CCR4_replicate1_t40

value: Yeast cells

value: 40 min

value: replicate 1

value: plus Auxin and Estradiol


title: Patient 6, PARCB transformed transition tumor cells, 6wks

value: Transition Tumor


title: Patient 6, PARCB transformed prostate organoid, 0wks

value: Prostate Organoid

value: Organoid


title: RKO cells, siCtrl-3

value: RKO

value: ANP32B wild type


title: WT_sh_5

description: Sample 5


title: HET1_D65

value: cell line

value: KOLF2-C1 human iPSC line

value: iPSC differentiated into dopaminergic neurons

value: LMX1A Cre AAVS1 BFP


title: RKO cells, siCtrl-1

value: human colorectal cancer cell


title: SCD +AID_POP2/CCR4_replicate1_t25

value: 25 min


title: SCD +AID_POP2/CCR4_replicate1_t35

value: 35 min


title: WT_sh_3

description: Sample 3

value: Heart

value: wildtype

value: sham


title: Patient 6, PARCB transformed early tumor cells, 4wks

value: Prostate

value: Xenograft

value: Early Tumor

value: PARCB transformation


title: WT_sh_2

description: Sample 2


title: Patient 6, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: WT_sh_4

description: Sample 4


title: SCD +AID_POP2/CCR4_replicate1_t20

value: Yeast cells

value: 20 min

value: replicate 1

value: plus Auxin and Estradiol


title: Patient 6, PARCB transformed transition tumor cells, 5wks

value: Transition Tumor


title: Patient 5, PARCB transformed endpoint tumor cells, 9wks

value: Endpoint Tumor


title: SCD +AID_POP2/CCR4_replicate1_t15

value: 15 min


title: SCD +AID_POP2/CCR4_replicate1_t30

value: 30 min


title: HC-3

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

institute: The Affiliated People’s Hospital of Jiangsu University

data_processing:
After Illumina sequeHCing, image analysis, and base recognition, the original reads after quality control were harvested. First use Q30 for quality control. Use cutadapt software (v1.9.3) to de-join the original reads, remove low-quality reads, and keep the reads with length> = 15 nt to get the de-connected reads (ie trimmed reads).
Then, the trimmed reads of all samples were combined, and new circRNA prediction was performed using miRDeep2 software (v2.0.0.5). Use Novoalign software (v3.02.12) to compare the trimmed reads of each sample to the combined human pre-circRNAs database (miRBase pre-circRNAs (v21) + newly predicted pre-circRNAs), allowing up to 1 mismatch.
Statistically compare the number of tags on each mature circRNA as the original expression level of the circRNA, and use TPM (tag counts per million aligned circRNAs) method for standardization. Calculate the Fold change between the two samples and screen for differentially expressed circRNAs. Calculate the P-value and Fold Change between the two groups of samples (with duplicates), and screen for differentially expressed circRNAs.
Assembly: human NBCI genobuild 36
Supplementary files format and content: Number of alignment tags per mature circRNA

source_name: serum exosomes

extract_protocol:
Human serum exosomes were isolated by density-gradient
centrifugation over Ficoll-Hypaque solution (Tianjin Haoyang Biological Technology Co., Tianjin, China) according to the manufacturer’s instructions and stored at -80 °C   until use for circRNA sequeHCing
RNA libraries were prepared for sequeHCing using standard Illumina protocols

tag: strain

value: Adult

value: Blood


title: Patient 5, PARCB transformed transition tumor cells, 8wks


title: HC-4


title: HC-5


title: SCD +AID_POP2/CCR4_replicate1_t10

value: 10 min


title: RKO cells, siCtrl-2

value: RKO

value: human colorectal cancer cell

value: ANP32B wild type


title: SCD +AID_POP2/CCR4_replicate1_t5

value: 5 min


title: WT_sh_1

description: Sample 1

value: Heart

value: wildtype

value: sham


title: Fetal intestinal organoids, rep 1

city: Pohang

first: Somi

last: Kim

address: 47, Jigok-ro

department: Life Sciences

country: South Korea

institute: POSTECH

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to mouse genome assembly GRCm39 via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with mouse gene annotation GRCm39.104.
Assembly: mm10
Supplementary files format and content: txt file containing expected counts (raw counts)
Supplementary files format and content: txt file containing TPM counts

source_name: small intestinal organoid

growth_protocol: 4-8 weeks of mice were harvested to isolate intestinal epithelial cells for adult intestinal organoids. E15.5 embryos were harvested to isolate intestinal epithelial cells for fetal intsetinal organoids. Both adult and fetal intestinal organoids were cultured with intesticult (STEMCELL Technologies) in vitro.

extract_protocol:
To isolate RNA from intestinal organoids, matrigel-embbed organoids were harvested with F12/DMEM, and then incubated with TrypLE at 37℃ for 15 min to remove matrigel. Dissociated cells were washed with DPBS three times. Total RNA was isolated using Easy-BLUETM RNA isolation kit (iNtRON Biotechnology, #17061).
total RNA was extracted with QIAzol reagent (Cat# 79306; QIAGEN) according to the manufacturer's instructions. The RNA-seq libraries were constructed using the NEXTflexTM Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer). Briefly, 1 μg of purified RNA was poly-A selected and fragmented with fragmentation enzyme. After first and second-strand synthesis from a template of poly-A selected/fragmented RNA, other procedures from adenylation to PCR amplification were done according to RNA-seq library construction steps.

tag: developmental stage

value: E15.5 embryo

value: small intestinal organoid

value: Epithelial cells


title: SCD +AID_POP2/CCR4_replicate1_t0

value: Yeast cells

value: 0 min

value: replicate 1

value: plus Auxin and Estradiol


title: HC-2

value: Adult


title: Patient 5, PARCB transformed early tumor cells, 4wks

value: Prostate

value: Xenograft

value: Early Tumor

value: PARCB transformation


title: iPSC, CTCF-del, 55

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

data_processing:
Quality of FASTQ files was quantified using FastQC, and adaptor sequences and low-quality reads were trimmed using Trim Galore. Alignment of the reads was done using STAR (hg38 genome build) and transcript quantification was performed using Salmon. The resulting count matrices were normalized by size factor and dispersion using the DESeq2 package in R (Love et al., 2014)
Assembly: GRCh38
Supplementary files format and content: .sf files is a salmon transcript abundance estimation file

source_name: iPSC

growth_protocol: iPSCs were cultured on tissue culture plastic coated with vitronectin in StemMACS iPS-Brew XF

extract_protocol: Library preparation was carried out using QuantSeq 3´-mRNA (Lexgon) according to the manufacturer's instructions. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).

treatment_protocol: CRISPR-cas 9 mediated CTCF deletion. Transfection of complexed crRNA-tracrRNA and Cas9 using the NEON transfection system using standard protocols.

value: iPSC

value: CTCF-del


title: Patient 5, PARCB transformed transition tumor cells, 6wks

value: Transition Tumor


title: Adult intestinal organoids, rep 2

value: 4-8 weeks adult


title: Adult intestinal organoids, rep 1


title: PTC-5

value: Blood


title: Patient 5, PARCB transformed prostate organoid, 0wks

value: Prostate Organoid

value: Organoid


title: Patient 5, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: Organoids, IR, day7, rep2

growth_protocol: 4-8 weeks of mice were harvested to isolate intestinal epithelial cells. Intestinal organoids were cultured with intesticult (STEMCELL Technologies) in vitro.

treatment_protocol: For IR samples, 6Gy X-ray was irradiated to intestinal organoids.

value: small intestinal organoid

value: Epithelial cells

value: 6Gy X-ray


title: PTC-4

value: Adult


title: iPSC, CTCF-del, 50


title: PTC-3


title: Patient 4, PARCB transformed transition tumor cells, 6.5wks

value: Prostate


title: Organoids, IR, day7, rep1


title: iPSC, WT, 102

value: WT


title: Patient 4, PARCB transformed transition tumor cells, 4.5wks

value: Xenograft


title: Patient 4, PARCB transformed endpoint tumor cells, 10wks

value: Endpoint Tumor

value: PARCB transformation


title: CTCF-del, 55

library_source: genomic

data_processing:
The Nextflow nf-core/chipseq pipeline (v2.0.0; https://doi.org/10.5281/zenodo.7139814) was used for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data together with Singularity containers
Assembly: GRCh38
Supplementary files format and content: narrowPeak files that provides called peaks of signal enrichment based on pooled, normalized data.

molecule: genomic DNA

extract_protocol:
iPSCs were fixed with 1% formaldehyde and fractionated using the Covaris M220 using Peak power 75W, Duty factor 5%, Cycle/burst 200 at 6 degrees for 25 minutes to obtain chromatin fractions  Immunoprecipitation was performed with the CTCF antibody using the ChIP-IT Express Chromatin Immunoprecipitation Kit (Activ Motiff) using standard protocols.
Illumina TruSeq Nano DNA Library Prep Kit, standard library preparation protocol

value: iPSC

tag: chip antibody

value: CTCF (Active Motif, #61311)


title: WT, iPSC_102


title: Organoids, Cont, day7, rep2


title: PTC-1


title: HC-1


title: Organoids, Cont, day7, rep1


title: PTC-2


title: Root tip, lbd quad 16h post cut, Rep 1

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

description: 10x Genomics

data_processing:
Sequences were processed using Cell Ranger 7.0.1
Each single cell sample was processed to remove ambient RNA using SoupX and doublet removed using DoubletFinder using the first 15 PCA dimensions. Cell profiles having more than 5% mitochondria or chloroplast gene expression exhibiting expression of CHLOROPHYLL A/B BINDING PROTEINs were removed. Reference single-cell data matrix was obtained from GEO Omnibus series GSE123818. Cells having less than 500 UMIs, more than 25,000 UMIs, less than 500 genes, or more than 10,000 genes were removed. Genes expressed in less than 10 cells or plastid genes were removed. The five samples were combined using Harmony and the first 20 dimensions of the PCA
Assembly: Araport11 genome annotation
Supplementary files format and content: Data matrix of expression data, normalized and filtered.
Supplementary files format and content: rds file of a seurat data object containing the single cell data and metadata

organism: Arabidopsis thaliana

source_name: Root tip

growth_protocol: Plants were germinate on 1/2 MS plates with 0.5% sucrose for 7 days in 16h/8h light/dark cycles at 22c

extract_protocol:
Primary roots tip (~1cm) were collected into a 35X10mm petri dish containing 60µl of cell wall digestion solution (3% w/v Cellulase, 1%w/v Macerozyme (Yakult), 0.4M Mannitol, 20mM MES, 0.02M KCl, Tris-HCl pH=5.7, heated to 55C° for 10min, cooled to room temperature followed by addition of 0.001 gr/ml BSA and 20mM CaCl2). Meristems were collected after 15min incubation and transferred to a fresh digestion solution for 1h. The solution was filtered twice through 40µm cell strainers and centrifuged for 10 minutes at 300g. Cells pellet were resuspended in washing solution (0.4 M mannitol, 20 mM MES, 20 mM KCl and 0.1% BSA) to a concentration of ~1000 cells/µl
Library was prepared according to the manufactorer instructions (10x genomics chromium 3' v2 protocol)

treatment_protocol: 7 days old plants were transferred to 5% agar plates and their root tip dissected with a dental needle. Plants were then moved back to 1/2MS plates and allowed to recover for 16h

value: Root tip

value: lbd6 lbd36 lbd12 lbd15

value: 16 hours after root tip dissection


title: Organoids, IR, day4, rep2


title: Patient 4, PARCB transformed prostate organoid, 0wks

value: Prostate Organoid

value: Organoid


title: CTCF-del, 50


title: Root tip, WT 16h post cut, Rep 2

description: 10x Genomics


title: Organoids, IR, day4, rep1


title: Root tip, lbd quad 16h post cut, Rep 2

description: 10x Genomics


title: Organoids, Cont, day4, rep1


title: Patient 7, PARCB transformed transition tumor cells, 9wks

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct)
Log normalization and data integration were pefromed using Seurat v3.2.3 (https://satijalab.org/seurat/articles/integration_introduction.html)
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each cell
Supplementary files format and content: tab-delimited text file contains Seurat log normalized counts for each cell
Supplementary files format and content: tab-delimited text file contains Seurat batch integrated counts for each cell

extract_protocol:
Tumors were dissociated into single cells, followed by cell sorting of triple colors (RFP, GFP and YFP) by flow cytometry
Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (Cat# PN1000123, 10x Genomics), Chromium Next GEM Chip G Single Cell Kit (Cat# PN1000120, 10x Genomics), and Single Index Kit T Set A (Cat# PN1000213, 10x Genomics) according to the manufacturer’s instructions. Briefly, cells were loaded to target 10,000 cells to form GEMs and barcode individual cells. GEMs were then cleaned cDNA and libraries were also created according to manufacturer’s instructions. Library quality was assessed using 4200 TapeStation System (Cat# G2991BA, Agilent) and D1000 ScreenTape (Cat# 5067-5582,  Agilent) and Qubit 2.0 (Cat# Q32866, Invitrogen) for concentration and size distribution.

value: Transition Tumor


title: Patient 7, PARCB transformed transition tumor cells, 7wks


title: Patient 3, PARCB transformed early tumor cells, 5wks

value: Early Tumor


title: Patient 4, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: CT26 cells, iRhom KO,  Rep2

city: Pittsburgh

first: Zhangyi

last: Luo

state: PA

address: 4041 Bigelow Blvd, Apt 112

institute: University of Pittsburgh

data_processing:
Data was analyzed by following HISAT2-Stringtie-Ballgown workflow published on Nature Protocol.(Pertea, M., Kim, D., Pertea, G. et al, Nat Protoc 11, 1650–1667 (2016).)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Colon cancer cells

growth_protocol: Both CT26 control or iRhom KO cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA prepared by University of Pittsburgh Sequencing Core
Library was prepared by University of Pittsburgh Sequencing Core

treatment_protocol: No treatment after KO

value: Colon cancer cells

value: iRhom KO


title: Patient 7, PARCB transformed endpoint tumor cells, 11wks

value: Prostate


title: CT26 cells, iRhom KO,  Rep1


title: Patient 3, human prostate basal cells, 0wks


title: Patient 3, PARCB transformed endpoint tumor cells, 18wks

value: Xenograft


title: Patient 6, PARCB transformed transition tumor cells, 6wks


title: Organoids, Cont, day4, rep2

value: small intestinal organoid

value: Epithelial cells


title: Organoids, cont, rep2

extract_protocol:
To isolate RNA from intestinal organoids, matrigel-embbed organoids were harvested with F12/DMEM, and then incubated with TrypLE at 37℃ for 15 min to remove matrigel. Dissociated cells were washed with DPBS three times. Total RNA was isolated using Easy-BLUETM RNA isolation kit (iNtRON Biotechnology, #17061).
One 1 µg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

treatment_protocol: 0.1 or 0.5 𝜇g/ml doxycline was treated in intestinal organoids for 3 days

value: Cont


title: Patient 3, PARCB transformed transition tumor cells, 7wks

value: PARCB transformation


title: Organoids, 0.1𝜇g/ml Dox, rep1

value: 0.1𝜇g/ml Doxycycline


title: Root tip, WT 16h post cut, Rep 1

description: 10x Genomics

value: Root tip

value: WT


title: Patient 2, PARCB transformed transition tumor cells, 9wks


title: Patient 6, PARCB transformed early tumor cells, 4wks


title: Organoids, 0.5𝜇g/ml Dox, rep2

value: 0.5𝜇g/ml Doxycycline


title: Patient 7, PARCB transformed early tumor cells, 5wks


title: Organoids, cont, rep1


title: Organoids, 0.5𝜇g/ml Dox, rep1


title: SMI-control_Biological rep 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
RTA 3.4.4
CLIP reads were de-duplicated, de-multiplexed, and trimmed to remove Illumina adapter sequences. Remaining reads shorter than 25 nt were discarded, and reads were 3'-trimmed down to a maximum of 35 nt. To assess differences in Chtop binding between the +Ex5 and ∆Ex5 isoforms, CLIP reads were mapped to the GENCODE vM11 annotation using tophat2 with default options. Reads overlapping the coding sequence (CDS), 5’UTR or 3’UTR of transcripts were counted for iCLIP-seq samples from both isoforms. Transcripts bound by either isoform were defined as having a minimum of 10 read counts in each of the biological replicates (+Ex or ∆Ex) for any of the CDS, 5’UTR or 3’UTR regions and having at least a >2-fold difference in average reads compared to the largest SMI control sample.
Assembly: mm10 (GENCODE vM11)
Supplementary files format and content: All files are in tab-delimited format. “ChtopCLIP_counts.3UTR.tab”, “ChtopCLIP_counts.5UTR.tab”, “ChtopCLIP_counts.CDS.tab” and “ChtopCLIP_counts.Total.tab” contain read counts mapping to each transcript section (5’UTR/3’UTR/CDS) as derived from the iCLIP-seq data. “ChtopCLIP_genePartLengths.tab” is a summary of the gene parts including the gene name and the length. “ChtopCLIP_DESeq2normCOUNTS_geneParts_combined.tab” contains normalized read counts as output from DESeq2 for each of the 5’UTR/CDS/3’UTR gene parts for all transcripts showing increased read counts in the Chtop∆Exon5 or Chtop+Exon5 pulldown samples compared to SMI controls (>10 minimum counts and >2 fold-change compared to the largest counts in the SMI controls). Transcripts annotated as enriched in either isoform pulldown were defined as having a >1 log2FoldChange (average normalized counts) between the isoform samples and a change in the same direction for each replicate.

source_name: N2a Flp-In rtTA

growth_protocol: Mouse neuroblastoma (N2a/N2a Flp-In rtTA) cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
iCLIP experiments were performed as previously described (Huppertz et al., 2014) with the addition of size-matched input (SMI) samples as negative controls (Van Nostrand et al., 2016). Cell pellets from crosslinked samples were lysed using ice cold lysis buffer (50 mM Tris–HCl, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate and 1 cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail tablet (Sigma Aldrich) per 10mL) at a 1:20 pellet weight to volume ratio (for 0.1g add 2.0 mL of lysis buffer) and sonicated. Lysates were divided into two 1 mL samples and treated with Turbo DNase (Thermo Fisher Scientiﬁc) and RNase I (Thermo Fisher Scientiﬁc) diluted 1/10 in PBS (HIGH RNase) or 1/50 in PBS (LOW RNase) for 5 minutes at 37°C to digest genomic DNA and partially digest RNA to short fragments of an optimal size range. RNA-protein complexes were purified using 100 µL of protein G Dynabeads (Thermo Fisher Scientiﬁc) and 2 μg of anti-Flag M2 (Sigma-Aldrich) antibody. 2% (20ul) of the total input lysate was retained for use as a SMI control. Following high salt washes, the immunoprecipitated RNA was 3′ end dephosphorylated and ligated to a pre-adenylated adaptor at the 3′ end overnight in a thermomixer (16 ºC), as described previously. The next day, 20% of the samples was 5′ end-labeled using radioactive ATP [γ-32P] and mixed with the unlabelled sample. The RNA-protein complexes from the immunoprecipitated and SMI samples were then separated on an SDS-PAGE gel and transferred to a nitrocellulose membrane overnight. RNA-protein complexes were isolated from the nitrocellulose membrane LOW RNase samples using the HIGH RNase samples as a reference (cut ~15-80 kDA above the protein length). RNA was recovered from the membrane by digesting the protein with proteinase k followed by phenol/chloroform extraction. SMI RNA samples were stored at -80 ºC until processing with 3’end adapter ligation and washes performed using MyOne Silane Dynabeads (Thermo Fisher Scientiﬁc) as per Van Nostrand et al., 2016.
The RNA was next converted into cDNA using sample specific barcoded primers containing a BamH1 restriction site to allow for multiplexing and digestion (see below). The cDNA was size selected on a 6% TBE-Urea gel using two length cut-offs (Mid: 80–100 nt and High: 100-150 nt) and then circularized to add the 5’end adapter using CircLigaseTm II (Cambio). Circularized cDNA was digested using BamH1 and then PCR amplified using Phusion™ High-Fidelity DNA Polymerase (Thermo Fisher Scientiﬁc). PCR cycle numbers were optimized for both the Mid and High size selected fragments for both isoform samples (23-25 cycles for Mid and 27 cycles for High). The final PCR libraries were purified by agarose gel electrophoresis using gel extraction columns (QIAGEN), and eluted DNA mixed at a ratio of 1:1 from the Mid, and High fractions for sequencing. For Chtop +Ex5 isoform samples the barcode primers used were Rt6clip (BR1), Rt14clip (BR2) and Rt13clip (BR3) while for ∆Ex5 Chtop samples the primers used were Rt1clip (BR1), Rt10clip (BR2) and Rt9clip (BR3). For SMI sample libraries Rt16clip (BR1, GFP_input), Rt15clip (BR2_∆Ex5_input), and Rt2clip (BR3_+Ex5_input) were used.
iCLIP-Seq

treatment_protocol: Doxycycline inducible N2a Flp-In rtTA cell lines expressing Chtop∆Ex5 or +Ex5 isoforms were grown in a 15 cm plate treated for 24 hours with 2 µg/mL Doxycycline (to induce cDNA expression) and crosslinked (0.15 J/cm2) at 254 nm with a Stratalinker 1800. Three independent biological replicates were used to generate iCLIP libraries for analysis (replicate samples harvested and processed on separate days).

value: N2a Flp-In rtTA

value: Mouse neuroblastoma

tag: cdna expressed_(n2a_flp-in_line)

tag: rt primer


title: Patient 2, PARCB transformed early tumor cells, 4wks

extract_protocol:
Tumors were dissociated into single cells, followed by cell sorting of triple colors (RFP, GFP and YFP) by flow cytometry. Total RNA was extracted from the cell lysates using miRNeasy kit (Cat# 217084, Qiagen).
Libraries for RNA-Seq of PARCB time course samples were prepared with KAPA Stranded mRNA-Seq Kit (Cat# KK8420, Roche). The workflow consists of mRNA enrichment and fragmentation.

tag: sample type

value: Early Tumor

tag: tumor collection_time


title: Patient 6, PARCB transformed endpoint tumor cells, 8wks

tag: tissue

value: Endpoint Tumor


title: Fetal intestinal organoids, rep 2

value: E15.5 embryo

tag: cell line


title: Organoids, 0.1𝜇g/ml Dox, rep2

tag: cell type

tag: genotype


title: CT26 cells, Control,  Rep2

value: Colon cancer cells

value: Control


title: Patient 2, PARCB transformed endpoint tumor cells, 12wks

value: Prostate


title: CT26 cells, Control,  Rep1


title: SMI-control_Biological rep 1


title: SMI-control_Biological rep 3

value: FLAG-GFP


title: Patient 2, PARCB transformed transition tumor cells, 7.5wks

value: Xenograft

value: Transition Tumor


title: Patient 5, PARCB transformed endpoint tumor cells, 9wks


title: Patient 3, PARCB transformed prostate organoid, 0wks

value: Prostate Organoid

value: Organoid


title: Patient 5, PARCB transformed transition tumor cells, 8wks

value: PARCB transformation


title: Patient 6, PARCB transformed transition tumor cells, 5wks


title: Patient 5, PARCB transformed transition tumor cells, 6wks


title: Patient 5, PARCB transformed early tumor cells, 4wks


title: Chtop_pEx5_iCLIP_BR2: N2a Flp-In rtTA (Chtop_withEx5), Biological rep 2


title: Patient 2, PARCB transformed prostate organoid, 0wks


title: Chtop_mEx5_iCLIP_BR3: N2a Flp-In rtTA (Chtop_withoutEx5), Biological rep 3


title: WT, iPSC_104

value: iPSC

value: CTCF (Active Motif, #61311)


title: Patient 1, PARCB transformed endpoint tumor cells, 12wks


title: Patient 1, PARCB transformed transition tumor cells, 8wks


title: Patient 1, PARCB transformed early tumor cells, 4wks


title: Patient 2, human prostate basal cells, 0wks

value: Prostate Basal Cells

value: Basal


title: Chtop_pEx5_iCLIP_BR1: N2a Flp-In rtTA (Chtop_withEx5), Biological rep 1

value: N2a Flp-In rtTA

value: Mouse neuroblastoma


title: adipocyte-siZNF189-3

type: RNA

city: Huddinge

first: Niklas

last: Mejhert

address: Blickagången 16

country: Sweden

institute: Karolinska Institute

hyb_protocol: 2.3 µg of ss cDNA target was hybridized to Clariom™ S Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific)

scan_protocol: Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol. The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific). For image processing software AGCC 4.0 was used.

data_processing: Microarray data were analyzed with packages available from R Bioconductor (http://www.bioconductor.org), R version 4.2.0.  Normalization and calculation of gene expression were performed with the Robust Multichip Average expression measure using the oligo package. Before further analysis, a nonspecific filter was applied to include only coding genes with log2 expression signal > 5 in at least 50% of all samples. To identify differentially expressed genes, the remaining 26787 transcripts were analyzed using the Linear Models for Microarray Data (limma) package (version 3.52.2) between two groups. Adjusted P value was used for statistical significance.

label: biotin

source_name: Primary adipocyte culture, 4 days after siRNA treatment

label_protocol: 100 ng of total RNA was used to generate amplified sense strand cDNA targets using GeneChip® WT Plus Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling

extract_protocol: RNA was isolated using Macherey-Nagel nucleospin RNA silica membrane purification kit REF740955

value: Adipocyte

value: ZNF189 depletion


title: Chtop_mEx5_iCLIP_BR2: N2a Flp-In rtTA (Chtop_withoutEx5), Biological rep 2


title: RNAseq, Williams 82, 16 hpi, inoculated3

status: Public on Nov 23 2023

city: Gainesville

first: Meixia

last: Zhao

state: FL

address: 1355 Museum Dr

institute: University of Florida

data_processing:
The quality of the sequenced reads was assessed using FastQC and the raw reads from the RNA-seq data were trimmed using Trimmomatic to remove adapters and low-quality reads
The trimmed reads were then aligned to the soybean reference genome, Williams 82 genome assembly v4.0 (Wm82.a4) using HISAT v2.2.1.
In addition, reads with multiple mapping matches were removed using COMEX 2 to retain uniquely mapped reads, and shortest alignments among multiple mapped reads or one alignment at random for each palindromic multiple mapping read if applicable.
The number of reads per gene for each sample was counted using HTSeq.
Assembly: Williams 82 genome assembly v4.0 (Wm82.a4)
Supplementary files format and content: Tab-delimited txt file including the HT-seq counts per gene for each sample.

organism: Glycine max

source_name: shoot

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plant Mini Kit.
Library construction was performed at Novogene.

value: shoot

value: Williams 82

value: P. sansomeana inoculation


title: Patient 2, PARCB transformed transition tumor cells, 9wks

value: Prostate


title: Patient 1, PARCB transformed prostate organoid, 0wks

data_processing:
TOIL pipeline v 3.12.0 (http://toil.ucsc-cgl.org/)
Sequence reads were trimmed for adaptor sequences/low-quality sequences using CutAdapt and FastQC from TOIL pipeline
Trimmed sequence reads were mapped to hg38 human genome using STAR from TOIL pipeline
Expected read counts were quantified using RSEM from TOIL pipeline
Upper quartile normalization and log transformation were performed on expected read counts
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains log2(upper quartile normalized counts + 1) for each sample


title: Chtop_pEx5_iCLIP_BR3: N2a Flp-In rtTA (Chtop_withEx5), Biological rep 3


title: RNAseq, Williams 82, 16 hpi, control2

value: control


title: Patient 2, PARCB transformed early tumor cells, 4wks

value: Xenograft

value: Early Tumor


title: adipocyte-siControl-3


title: adipocyte-siControl-4


title: Chtop_mEx5_iCLIP_BR1: N2a Flp-In rtTA (Chtop_withoutEx5), Biological rep 1


title: Patient 1, human prostate basal cells, 0wks


title: RNAseq, Williams 82, 8 hpi, control3


title: RNAseq, Williams 82, 4 hpi, inoculated3


title: RNAseq, Williams 82, 8 hpi, inoculated2


title: RNAseq, Williams 82, 4 hpi, inoculated2


title: RNAseq, Senaki, 16 hpi, inoculated3

value: Senaki


title: RNAseq, Williams 82, 2 hpi, inoculated3


title: RNAseq, Senaki, 16 hpi, inoculated2


title: RNAseq, Williams 82, 16 hpi, control3


title: adipocyte-siZNF189-1


title: RNAseq, Senaki, 16 hpi, control2


title: RNAseq, Williams 82, 4 hpi, control2


title: RNAseq, Senaki, 16 hpi, control3


title: RNAseq, Senaki, 8 hpi, inoculated2


title: RNAseq, Williams 82, 2 hpi, control3


title: RNAseq, Senaki, 8 hpi, inoculated3


title: RNAseq, Senaki, 2 hpi, inoculated3


title: RNAseq, Senaki, 8 hpi, control2


title: RNAseq, Senaki, 4 hpi, inoculated3


title: RNAseq, Senaki, 2 hpi, control3


title: RNAseq, Senaki, 4 hpi, control3


title: RNAseq, Senaki, 4 hpi, inoculated2


title: RNAseq, NE2701, 16 hpi, inoculated2


title: RNAseq, NE2701, 16 hpi, inoculated3


title: RNAseq, Senaki, 4 hpi, control2


title: RNAseq, NE2701, 16 hpi, control2


title: RNAseq, NE2701, 16 hpi, control3


title: RNAseq, Senaki, 2 hpi, inoculated2


title: RNAseq, Williams 82, 4 hpi, control3


title: RNAseq, Senaki, 2 hpi, control2


title: RNAseq, NE2701, 4 hpi, inoculated3


title: RNAseq, NE2701, 8 hpi, inoculated2


title: RNAseq, NE2701, 2 hpi, control3


title: RNAseq, NE2701, 4 hpi, control2


title: RNAseq, NE2701, 2 hpi, inoculated3


title: RNAseq, NE2701, 2 hpi, inoculated2


title: RNAseq, NE2701, 4 hpi, control3


title: RNAseq, NE2701, 2 hpi, control2


title: RNAseq, Colfax, 16 hpi, inoculated2

value: Colfax


title: RNAseq, Colfax, 16 hpi, control2


title: RNAseq, Colfax, 16 hpi, control3


title: RNAseq, Colfax, 8 hpi, inoculated3


title: RNAseq, NE2701, 8 hpi, inoculated3


title: RNAseq, NE2701, 8 hpi, control2


title: RNAseq, Colfax, 4 hpi, inoculated3


title: RNAseq, Colfax, 4 hpi, inoculated2


title: RNAseq, Colfax, 2 hpi, inoculated3


title: RNAseq, Colfax, 4 hpi, control3


title: RNAseq, Colfax, 2 hpi, inoculated2


title: RNAseq, Colfax, 4 hpi, control2


title: RNAseq, NE2701, 4 hpi, inoculated2


title: RNAseq, Colfax, 2 hpi, control3


title: WGBS, Williams 82, 4 hpi, inoculated4

data_processing:
The raw reads were quality controlled by FastQC and trimmed using Trimmomatic.
The resulting clean reads were then mapped to the soybean reference genome v4.0 (Wm82.a4) using Bismark with the following parameters (-n 2, -I 50, -N 1).
To eliminate PCR duplicates, the deduplication package under Bismark was utilized.
Additional packages including Bismark methylation extractor, bismark2bedGraph and coverage2cytosine under Bismark were employed to extract the methylated cytosines and count methylated and unmethylated reads.
Assembly: Williams 82 genome assembly v4.0 (Wm82.a4)
Supplementary files format and content: Tab-delimited txt file including the number of methylated reads and unmethlyated reads per each of cytosine contexts for each sample

extract_protocol:
DNA was isolated using the modified CTAB method.
Library construction was performed at Novogene.


title: WGBS, Williams 82, 4 hpi, control1


title: WGBS, Williams 82, 4 hpi, control4


title: RNAseq, Colfax, 2 hpi, control2


title: RNAseq, Colfax, 8 hpi, control2


title: RNAseq, Colfax, 8 hpi, inoculated2


title: WGBS, Williams 82, 16 hpi, inoculated1


title: WGBS, Williams 82, 16 hpi, control4


title: WGBS, Williams 82, 16 hpi, inoculated4


title: WGBS, Colfax, 4 hpi, inoculated4


title: WGBS, Colfax, 4 hpi, inoculated1


title: WGBS, Colfax, 4 hpi, control1


title: WGBS, Colfax, 4 hpi, control4


title: WGBS, Colfax, 16 hpi, inoculated1


title: WGBS, Colfax, 16 hpi, inoculated4


title: RNAseq, Williams 82, 8 hpi, inoculated1


title: WGBS, Colfax, 16 hpi, control4


title: RNAseq, Williams 82, 8 hpi, control2


title: RNAseq, Williams 82, 2 hpi, inoculated2


title: WGBS, Colfax, 16 hpi, control1


title: RNAseq, NE2701, 8 hpi, control3


title: WGBS, Williams 82, 16 hpi, control1


title: RNAseq, Williams 82, 2 hpi, control2


title: RNAseq, Colfax, 16 hpi, inoculated3


title: RNAseq, Colfax, 8 hpi, control3


title: RNAseq, Williams 82, 16 hpi, inoculated2


title: gd7 5h ATAC Replicate 2

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

department: Dept. of Molecular Biosciences

institute: Stockholm University

description: Sequenced genomic DNA tagged by Tn5

data_processing:
ATAC-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. RPKM normalized ATAC-seq coverage tracks were generated using the deepTools (v.3.5.1) package (default parameters with binSize = 2 (bases), normalizeUsing RPKM). Bigwig files of the mean RPKM were produced using the deepTools 'bigwigCompare' tool.
Assembly: dm6
Supplementary files format and content: bigwigs for coverage

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Toll mutant (from gd7, Tollrm9/rm10 and Toll10B) embryos were collected from flies kept on potato-mash agar food and maintained at 25 degrees Celsius. Embryos were collected on apple juice plates with fresh yeast and aged at 25 degrees Celsius until they reached the range of hours after egg laying (AEL) for the required developmental stage.

extract_protocol:
Hand-sorted embryos were dechorionated in dilute bleach, rinsed thoroughly in embryo wash buffer (PBS, 0.1% Triton X-100) and crude nuclear extracts isolated by homogenizing the embryos using a motor pestle in ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifugating at 700 g for 10 min. The nuclear pellet was resuspended in 22.5 μl of ATAC lysis buffer, 2.5 μl Tn5 (Tagment DNA Enzyme 1 (TDE) (Illumina)) and 25 μl Tagment DNA Buffer (Illumina) and subjected to tagmentation at 37°C on a thermomixer at 1,000 rpm. Transposition was blocked by the addition of 1% SDS and DNA purified with Agencourt AMPure XP beads (Beckman Coulter, A63881) according to the manufacturer’s instructions using a 2:1 ratio of beads to sample.
Libraries were prepared as previously described in 'Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome positions. Nat Methods 10, 1213-1218.'. Briefly, tagmented DNA was PCR amplified using 1x Phusion® High-Fidelity PCR Master Mix with GC Buffer (NEB) and 1.25 μM i5 and i7 PCR primers (Nextera® Index Kit (Illumina)) with the following PCR amplification conditions: 72°C for 5 min, followed by 10 cycles of 98°C for 10 seconds, 65°C for 1 min and 15 seconds, then 72°C for 1 min. Amplified libraries were purified with Agencourt AMPure XP beads with a 1.5:1 ratio of bead to sample volume. Libraries prepared from biological triplicates were sequenced paired-end (2 x 150 bp) on the Illumina NovaSeq platform at SciLifeLab, Stockholm. ATAC-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. RPKM normalized ATAC-seq coverage tracks were generated using the deepTools (v.3.5.1) package. Bigwig files of the mean RPKM were produced using the deepTools 'bigwigCompare' tool.

treatment_protocol: Toll mutant embryos were collected for 0.5 h and aged accordingly to achieve three developmental time points: 2.5-3 h, 3.5-4 h and 4.5-5 h AEL. For each time point, 10 embryos per replicate presenting the correct morphology for the developmental stage sought were immediately hand-sorted.

value: Early embryonic stage (5 h AEL)

value: embryos

value: gd7 mutant


title: Tollrm9/rm10 4h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (4 h AEL)

value: Tollrm9/rm10 mutant


title: Tollrm9/rm10 3h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (3 h AEL)


title: Tollrm9/rm10 3h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: Tollrm9/rm10 3h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 5h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Toll10B mutant


title: Tollrm9/rm10 4h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: Tollrm9/rm10 5h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: Tollrm9/rm10 4h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 4h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 4h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Tollrm9/rm10 5h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Tollrm9/rm10 5h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 3h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 5h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 3h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 4h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 3h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 5h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: gd7 5h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: gd7 5h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: gd7 4h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: gd7 3h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: gd7 3h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: gd7 4h ATAC Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: gd7 4h ATAC Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: gd7 3h ATAC Replicate 3

description: Sequenced genomic DNA tagged by Tn5


title: RNAseq, Senaki, 8 hpi, control3


title: Mice 110, scRNA-Seq

city: Heidelberg

first: Kwong Leong

last: Wong

state: Germany (DEU)

address: Im Neuenheimer Feld 280

department: Molecular genetics

institute: DKFZ

description: 10x Genomics

data_processing:
Cellranger 5.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
Spleen single-cell suspensions were generated by using the gentleMACS tissue dissociator with Gentle MACS tubes C (Miltenyi Biotec). Erythrocytes were lysed by using Red blood cell lysis buffer (Mitenyi Biotec). Samples were stained for cell surface proteins for 30 min. After washing with PBS, cells were resuspended in PBS + 5 % FBS containing 0.2 μg/mL DAPI prior cell sorting.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: T cells and CLL leukemic cells

value: spleen

value: TCL1 adoptive transfer

tag: age

value: 4 months


title: Mice 107, scVDJ-Seq

description: 10x Genomics

data_processing:
Cellranger 5.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scVDJ-seq


title: Mice 107, scRNA-Seq

description: 10x Genomics


title: Mice 110, scVDJ-Seq

description: 10x Genomics


title: FAPs_480

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition

data_processing:
The trimming was done with Trimgalore, the alignment was performed with STAR and the gene counting was done with featureCounts.
Assembly: mm10
Supplementary files format and content: tab-seperated value files

source_name: skeletal muscle

extract_protocol:
Muscle samples were isolated, minced and digested using Collagenase A for 45 min at 37 °C. Dispase II was added for 30 minutes to the muscle lysates. Muscles slurries were passed 10 times through a syringe and cell strainer and centrifugated. The pellet was re-suspended in Ammonium Chloride Potassium lysis buffer to eliminate red blood cells and centrifuged again. Cells were re-suspended in sorting buffer consisting of 100 µl Hank´s balanced salt solution (HBSS) containing 0.4% FBS. Fibro-adipogenic progenitors were isolated freshly using fluorescence-activated cell sorting (FACS) using the following surface marker profile: CD45-CD11b-CD31-SCA1+. For each single cell library, 4 independent chips using a commercial microfluidics platform (IFC, Fluidigm) were used with a capacity of capturing up to 96 individual cells per loaded chip. For each chip loading, cells were pooled from three mice (i.e. 4 pools per experimental group). Individual cell quality was checked as per manufacturers’ recommendation.
Successfully captured cells and corresponding cDNA samples of individuals cells were subsequently processed by Smart-Seq2 cDNA library preparation (Clontech) using the Nextera XT Indexing kit (Illumina). Quality control was performed using an Agilent Bioanalyzer DNA High Sensitivity Kit for electropherogram tracing.

value: skeletal muscle

value: Fibro-adipogenic progenitors

tag: treatment

value: aged


title: E16.5_Stab_bcat_mammary_rep5

city: Bristol

first: Qiang

last: Lan

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

institute: University of Bristol

description:
Sample_4
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds

data_processing:
All sequencing reads were processed for quality control, removal of low-quality reads, adaptor sequence and ribosomal RNA using fastqc version 0.11.8 , multiqc version 1.9 , Trimmomatic version 0.39 and SortMeRNA version 2.1 . The transcript alignment was performed with Salmon version 0.99.0 to the reference genome (mm10).
The filtered reads were mapped to the reference genome (mm10) using Salmon version 0.99.0
Read counts were extracted and normlized using tximport (1.15.10) and DESeq2 (3.15).
Assembly: mm10
Supplementary files format and content: tab separated, normalized counts
Supplementary files format and content: tab separated, raw counts
Supplementary files format and content: R object for DESeq2 analysis

source_name: E16.5 mammary epithelium

extract_protocol:
Tissues from each embryo were lysised in 150µl TRI Reagent (Merck) and stored in -80. samples from 2-3 embryos from the same litter with same genotype were pooled together as one sample before RNA extraction. The total volume of TRI Reagent for each sample was adjusted to 750 µl. After homogenization, 150 µl chloroform was added to each sample. The sample was mixed by gentle inverting the tubes and then incubated for 15 mins in RT. After 15 minutes centrifugation at 4 degrees with the speed of 12,000g, the aqueous phase was carefully transferred into a new tube. Repeat chloroform separation step once more to increase the purity of the RNA samples. Equal volume of 70% Ethanol was lowly added to the obtained aqueous phase and mixed gently by inversion. Use RNeasy MiniElute spin column (Qiagen) to further purify the total RNA following the manual of the manufacturer. The purified RNA was eluted with 20 µl RNase-free water and stored in -80.  RNA concentration was measured with Qubit RNA HS Assay Kit (Q32855, Thermo Fisher) using Qubit 4 Fluorometer (Thermo Fisher).
cDNA libraries were prepared with Ovation SoLo RNA-seq System (NuGen/Tecan Genomics) according to manufacturer's instructions

value: mammary epithelium

value: mix of C57Bl/6 and NMRI

value: stab-Beta-cat

tag: Sex

value: female


title: adipocyte-siZNF189-2

value: Adipocyte

value: ZNF189 depletion


title: WGBS, Williams 82, 4 hpi, inoculated1

value: shoot

value: Williams 82

value: P. sansomeana inoculation


title: E13.5_Stab_bcat_mammary_rep4

description:
Sample_18
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds

source_name: E13.5 mammary epithelium

value: not applicable


title: E16.5_WT_mammary_rep2

description:
Sample_24
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds

value: control


title: E16.5_WT_mammary_rep1

description:
Sample_23
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: adipocyte-siControl-2


title: adipocyte-siZNF189-4


title: FAPs_475


title: FAPs_479

value: young


title: FAPs_477


title: FAPs_478


title: FAPs_476


title: Total muscle, post-injury, aged

data_processing:
The demultiplexing, barcoded processing and gene counting using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tab-separated value files

extract_protocol:
Muscles samples were isolated, minced and digested using Collagenase A for 45 min at 37 °C. Dispase II was added for 30 minutes to the muscle lysates. Muscles slurries were passed 10 times through a syringe and cell strainer and centrifugated. The pellet was re-suspended in Ammonium Chloride Potassium lysis buffer to eliminate red blood cells and centrifuged again. Cells were re-suspended in sorting buffer consisting of 100 µl Hank´s balanced salt solution (HBSS) containing 0.4% FBS. Living cells were gated for the accumulation of Calcein blue and the exclusion of propidium iodide (PI) fluorescence. Alive mononucleated (i.e. non-myofiber) cells sorted and pooled from three mice per sample to obtain heterogeneous populations including all muscle-resident viable cells. Cells were encapsulated as Gel Beads-in-emulsion (GEM) and samples were processed using the 10x Genomics Chromium Controller platform as per manufacturers’ guidelines.
Single cell-cDNA libraries were processed according to the Chromium Next GEM Single Cell 3' Kit v3.1 library construction workflow, and quality-controlled using an Agilent Bioanalyzer DNA High sensitivity Kit electropherogram tracing.


title: Total muscle, post-injury, young


title: E13.5_Stab_bcat_mammary_rep3

description:
Sample_17
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E13.5_Stab_bcat_mammary_rep1

description:
Sample_15
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E13.5_WT_mammary_rep4

description:
Sample_8
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E13.5_WT_mammary_rep1

description:
Sample_12
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E16.5_Stab_bcat_mammary_rep2

description:
Sample_25
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E16.5_WT_mammary_rep4

description:
Sample_31
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E16.5_Stab_bcat_mammary_rep4

description:
Sample_35
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E13.5_WT_mammary_rep3

description:
Sample_7
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: FAPs_474


title: E13.5_WT_mammary_rep2

description:
Sample_14
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E13.5_Stab_bcat_mammary_rep2

description:
Sample_16
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E16.5_WT_mammary_rep5

description:
Sample_32
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E16.5_Stab_bcat_mammary_rep1

description:
Sample_21
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: FAPs_472


title: FAPs_473


title: FAPs_470


title: FAPs_471


title: E16.5_WT_mammary_rep3

description:
Sample_3
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: E16.5_Stab_bcat_mammary_rep3

description:
Sample_26
normalized_counts_matrix.txt
raw_counts_matrix.txt
Deseq_dds_txi.rds


title: adipocyte-siControl-1


title: FAPs_468


title: FAPs_469


title: FAPs_467


title: FAPs_466


title: FAPs_465


title: FAPs_464


title: FAPs_463


title: FAPs_462


title: FAPs_460


title: FAPs_461


title: FAPs_458


title: FAPs_457


title: FAPs_455


title: FAPs_445


title: FAPs_442


title: FAPs_443


title: FAPs_456


title: FAPs_447


title: FAPs_446


title: FAPs_444


title: FAPs_441


title: FAPs_459


title: FAPs_438


title: FAPs_437


title: FAPs_452


title: FAPs_453


title: FAPs_451


title: FAPs_448


title: FAPs_440


title: FAPs_435


title: FAPs_449


title: FAPs_436


title: FAPs_450


title: FAPs_454


title: FAPs_430


title: FAPs_433


title: FAPs_432


title: FAPs_439


title: FAPs_431


title: FAPs_434


title: FAPs_429


title: FAPs_428


title: FAPs_426


title: FAPs_425


title: FAPs_422


title: FAPs_423


title: FAPs_420


title: FAPs_421


title: FAPs_424


title: FAPs_418


title: FAPs_419


title: FAPs_416


title: FAPs_413


title: FAPs_410


title: FAPs_406


title: FAPs_412


title: FAPs_408


title: FAPs_407


title: FAPs_411


title: FAPs_415


title: FAPs_414


title: FAPs_401


title: FAPs_400


title: FAPs_404


title: FAPs_405


title: FAPs_402


title: FAPs_427


title: FAPs_399


title: FAPs_398


title: FAPs_397


title: FAPs_396


title: FAPs_417


title: FAPs_409


title: FAPs_394


title: FAPs_391


title: FAPs_388


title: FAPs_392


title: FAPs_395


title: FAPs_385


title: FAPs_384


title: FAPs_381


title: FAPs_393


title: FAPs_389


title: FAPs_386


title: FAPs_383


title: FAPs_379


title: FAPs_387


title: FAPs_382


title: FAPs_380


title: FAPs_377


title: FAPs_375


title: FAPs_376


title: FAPs_374


title: FAPs_373


title: FAPs_378


title: FAPs_372


title: FAPs_371


title: FAPs_390


title: FAPs_370


title: FAPs_368


title: FAPs_369


title: FAPs_367


title: FAPs_366


title: FAPs_365


title: FAPs_361


title: FAPs_362


title: FAPs_360


title: FAPs_363


title: FAPs_364


title: FAPs_359


title: FAPs_355


title: FAPs_357


title: FAPs_356


title: FAPs_353


title: FAPs_352


title: FAPs_350


title: FAPs_351


title: FAPs_347


title: FAPs_346


title: FAPs_345


title: FAPs_403


title: FAPs_349


title: FAPs_341


title: FAPs_342


title: FAPs_354


title: FAPs_348


title: FAPs_344


title: FAPs_358


title: FAPs_339


title: FAPs_340


title: FAPs_338


title: FAPs_336


title: FAPs_337


title: FAPs_334


title: FAPs_332


title: FAPs_333


title: FAPs_331


title: FAPs_343


title: FAPs_329


title: FAPs_328


title: FAPs_325


title: FAPs_327


title: FAPs_324


title: FAPs_323


title: FAPs_322


title: FAPs_321


title: FAPs_320


title: FAPs_317


title: FAPs_319


title: FAPs_315


title: FAPs_316


title: FAPs_314


title: FAPs_335


title: FAPs_313


title: FAPs_310


title: FAPs_312


title: FAPs_309


title: FAPs_307


title: FAPs_311


title: FAPs_308


title: FAPs_330


title: FAPs_304


title: FAPs_306


title: FAPs_326


title: FAPs_303


title: FAPs_318


title: FAPs_301


title: FAPs_300


title: FAPs_299


title: FAPs_298


title: FAPs_296


title: FAPs_305


title: FAPs_294


title: FAPs_297


title: FAPs_293


title: FAPs_292


title: FAPs_291


title: FAPs_295


title: FAPs_302


title: dRNAseq_plus TEX treatment replicate i

city: Jena

first: Marcel

last: Sprenger

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

data_processing:
Sequencing of the cDNA libraries was performed by Vertis Biotechnologie AG i.L. company, Freising, Germany
cDNA reads were imported into CLC Genomics Workbench v20.0 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, Trim quality scores limit 0.05, Trim ambiguous nucleotides 2
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = both, Maximum number of hits for a read = 1, expression value: TPM
Computation of coverage and difference between neighboring nucleotides, local maxima of differences were annotated as TSS, manual curation of predicted TSS, DOI: 10.5281/zenodo.8388882
Assembly: NC_002505, NC_002506, NC_009016.1

organism: Vibrio cholerae

growth_protocol: Vibrio cholerae C6706  Δtdh + JSP1269 were grown overnight in M9 minimal media, supplemented with 0.4% glucose. The following day bacteria were diluted 1:200 in fresh media. At OD 0.4, cells were back-diluted 1:10 in M9 with 0.4% glucose and 0.035% arabinose to induce VqmA phage and grow again to OD 0.2. Induction of phage VP882 was activated by addition of 25 µM DPO to V. cholerae. Samples were collected (pre, 15min, 60 min, 120 min post induction)

extract_protocol:
RNA was isolated using Tri-reagent. Prepared RNA was digested for DNA contaminations (TurboDNase treatment) and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed by Vertis Biotechnologie AG i.L. company, Freising, Germany.
The rRNA depleted RNAs samples were fragmented using ultrasound (4 pulses of 30 sec at 4°C). Then an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. PCR cycles performed and barcode sequences, which are part of the 5' and 3' sequencing adapters, are included in Table 2. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). cDNA from +/- TEX treated RNA: First, the total RNA samples Nr. 31 – 33 were fragmented using ultrasound (4 pulses of 30 sec at 4°C).This was followed by a treatment with T4 Polynucleotide Kinase (NEB). The samples were then split into two halves and one half was subjected to Terminator Exonuclease treatment (+TEX; Lucigen), the other half was left untreated (-TEX). The RNA samples were poly(A)-tailed using poly(A) polymerase. Then, the 5'PPP structures were removed using RNA 5' Polyphosphatase (Lucigen). Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. PCR cycles performed and barcode sequences, which are part of the 5' and 3' sequencing adapters, are included in Table 2. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: The bacteria were treated with 25 µM final concentration of 3,5-dimethylpyrazin-2-ol (DPO). 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethananol, 5% phenol).

tag: time

value: replicate 1

value: delta_tdh + JSP-1269 (VP882::kanR)

value: dRNA-seq

value: with TEX treatment


title: dRNAseq_plus TEX treatment replicate iii

value: replicate 3


title: RNAseq_120 min replicate iii

value: 120 min

value: RNA-seq


title: dRNAseq_minus TEX treatment replicate i

value: without TEX treatment


title: dRNAseq_minus TEX treatment replicate iii


title: dRNAseq_minus TEX treatment replicate ii

value: replicate 2


title: dRNAseq_plus TEX treatment replicate ii


title: FAPs_290

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: RNAseq_120 min replicate i


title: RNAseq_60 min replicate iii

value: 60 min


title: RNAseq_60 min replicate i


title: RNAseq_60 min replicate ii


title: RNAseq_15 min replicate i

value: 15 min


title: RNAseq_15 min replicate ii


title: RNAseq_120 min replicate ii


title: RNAseq_pre replicate iii

value: 0 min


title: RNAseq_pre replicate ii


title: RNAseq_15 min replicate iii


title: FAPs_289

value: aged


title: FAPs_288


title: RNAseq_pre replicate i


title: FAPs_287


title: QR_3d3

city: Being

first: Li

last: Xueyan

address: No.35, Qinghua Eastern Road, Haidian

department: The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry

institute: Beijing Forestry University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: FPKM, count

organism: Cytospora chrysosperma

source_name: Cytospora chrysosperma

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: time point

value: Inoculation 3 days


title: QR_3d2


title: QR_1d1

value: Inoculation 1 days


title: QR_1d3


title: QR_1d2


title: FAPs_284

value: young


title: FAPs_285


title: FAPs_283


title: QR_0d2

value: Inoculation 0 days


title: FAPs_281


title: FAPs_280


title: QR_0d1


title: FAPs_279


title: FAPs_277


title: FAPs_275


title: FAPs_276


title: FAPs_274


title: FAPs_273


title: FAPs_286


title: FAPs_278


title: FAPs_272


title: JXY, replicate2

city: Fuzhou

first: Zhiyun

last: Cao

state: 福建Fujian

address: 1# Qiu Yang Road

institute: Fujian university

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3)
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0)  with default parameters
The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: mm 10
Supplementary files format and content: tab-delimited text files including raw counts data for each samples

source_name: Human colon

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen),1 μg total RNA meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces

value: Human colon

value: epithelial cells

value: ras mutation

value: JXY treatment


title: DMSO, replicate3

value: DMSO as control


title: JXY, replicate4


title: FAPs_282


title: QR_3d1


title: QR_0d3


title: JXY, replicate3


title: E45_Bla_mzKO_CDX2_CR_rep1

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data
Library strategy: CUT&RUN

source_name: E4.5 blastocyst

growth_protocol: For collection of wildtypes E4.5 blastocyst, 4–6-week-old female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with malemice. E4.25 blastocyst were flushed out from the uterus at E4.25.

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2 × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Tfap2c mzKO

value: mix

value: E4.5 blastocyst

value: mzKO


title: DMSO, replicate2


title: E45_Bla_mzKO_CDX2_CR_rep2


title: FAPs_270

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: DMSO, replicate1


title: FAPs_268


title: FAPs_271


title: FAPs_267


title: E45_Bla_control_CDX2_CR_rep2

value: Tfap2c control

value: control


title: JXY, replicate1


title: DMSO, replicate4


title: E45_Bla_control_CDX2_CR_rep1


title: FAPs_265


title: FAPs_266


title: Input, DRIP, LUAD, PC-9

city: Guiyang

first: Fuzhou

last: Tang

state: Guizhou

address: Dangwu Town

institute: Guizhou Medical University

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequencing quality were examined using FastQC software.
The 5’, 3’-adaptor bases were trimmed using cutadapt software.
The trimmed reads were aligned to human reference genome GRCh38 using bowtie2 software.
The aligned reads were used for peak calling of the DRIP regions using MACS2.
Statistically significant DRIP-enriched peaks were identified at a p-value threshold of 0.001. The peaks were annotated with the overlapping or nearest gene. Differentially accessible peaks were analyzed using DiffBind.
Assembly: hg38
Supplementary files format and content: Tab-delimited xlsx file with peak annotation and  peak counts.

extract_protocol:
Genomic DNA Extraction & Fragmentation: Total nucleic acids were extracted from cells by SDS/proteinase K treatment followed by phenol-chloroform extraction and ethanol precipitation. More than 10 µg genomic DNA for each sample was fragmented by ultrasound (Perform 10-15 cycles of 30 s ON/ 30 s OFF, spin after 3, 6, 9, and 12 cycles to ensure homogeneous sonication). DRIP immunoprecipitation: The fragmented DNA was divided equally into “IgG”, and “RIP” aliquots. Each of the two aliquots was mixed with 1 µL the synthetic RNA̢DNA hybrid spike-ins. “DRIP” was immunoprecipitated with 20 µg S9.6 antibody bound to protein G resin, “lgG” was immunoprecipitated with 20 µg non-immune IgG instead. The reactions were incubated at 4°C for overnight with head-over-tail rotation. The beads were washed three times with binding buffer and eluted in 250 µL elution buffer at 50°C for 30 min with rotation. The eluted DNAs were cleaned up by phenol chloroform and eluted in 15 µl ddH2O.
DRIP-seq library preparation: Followed by second DNA strand synthesis. The materials were cleaned up with 1.8X volume of DNA Beads and ligate “A” and adaptor. Add 10 µl ddH2O and 35 µl PEG/NaCl (1:1) to clean up and eluted with 10 µl ddH2O. Add 11 µl KAPA HiFi HotStart ReadyMix (2X) and 1 µl primers to amplify library. Each DNA library was amplified 9-20 cycles depending on the starting material amount. The library DNA was purified by 0.8X volume of DNA Beads. The library concentration and size distribution were checked by Qubit and agarose gel.

value: Human lung adenocarcinoma

tag: antibody

tag: cancer type

value: LUAD

tag: group

value: input


title: FAPs_263

value: young


title: FAPs_264

value: aged


title: Exp_2, DRIP, LUAD, PC-9

value: S9.6 antibody

value: exp


title: Exp_1, DRIP, LUAD, PC-9


title: FAPs_262


title: FAPs_260


title: FAPs_261


title: Control_2, DRIP, LUAD, PC-9


title: Control_1, DRIP, LUAD, PC-9


title: FAPs_269


title: 4cell_control_RNA_rep1

data_processing:
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data

source_name: 4-cell stage

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to males.

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.

tag: strain


title: FAPs_258


title: FAPs_259


title: 4cell_control_RNA_rep2


title: 2cell_mzKO_RNA_rep2

source_name: 2-cell stage


title: HMEC-1 cells, 50µM TMAO, 48H, 3

city: Singapore

first: Meyammai

last: Shanmugham

address: 8 Somapah Road

department: Science, Mathematics, and Technology

country: Singapore

institute: Singapore University of Technology and Design

data_processing:
nf-core RNAseq bioinformatics pipeline version 3.6 to generate the read counts for downstream analyses.
Sequence reads were trimmed using Trim Galore to trim off the low quality bases from the ends of the reads to increase mapping efficiency
Trimmed sequences are mapped against Hg39 for the pair-end library
Read count extraction and normalisation were performed
Assembly: Hg39
Supplementary files format and content: raw counts

extract_protocol:
HMEC-1 were lysed, and total RNA was extracted using the AurumTM Total RNA Mini Kit.
Total RNA from treated HMEC-1 was used to construct libraries using the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina NR605.

value: Human Microvascular Endothelial Cells-1

value: 50µM TMAO


title: FAPs_257


title: FAPs_256


title: HMEC-1 cells, 50µM TMAO, 48H, 2


title: FAPs_254


title: FAPs_253


title: HMEC-1 cells, 50µM TMAO, 48H, 1


title: 4cell_mzKO_RNA_rep2

value: Tfap2c mzKO


title: 2cell_control_RNA_rep2

value: mix


title: 4cell_mzKO_RNA_rep1


title: 2cell_mzKO_RNA_rep1


title: FAPs_251


title: 2cell_control_RNA_rep1


title: HMEC-1 cells, CTRL, 3

value: Control


title: FAPs_250


title: FAPs_247


title: FAPs_248


title: FAPs_246


title: FAPs_255


title: FAPs_249


title: HMEC-1 cells, CTRL, 1


title: HMEC-1 cells, 50µM TMAO, 24H, 3


title: FAPs_243


title: E45_TE_mzKO_RNA_rep2

source_name: E4.5 TE

growth_protocol: For collection of wildtypes E4.25 blastocyst, 4–6-week-old  female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with malemice. E4.25 blastocyst were flushed out from the uterus  at E4.25.


title: E45_TE_control_RNA_rep2


title: HMEC-1 cells, 50µM TMAO, 24H, 2


title: FAPs_244


title: E45_TE_mzKO_RNA_rep1


title: FAPs_242


title: E45_TE_control_RNA_rep1

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before be_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0004_ആ߻倀므羰_x0000__x0000__x0000__x0000__x0000_饒୥


title: FAPs_241


title: E65_ExE_mzKO_RNA_rep5

source_name: E6.5 ExE

growth_protocol: E5.5 -E7.5 embryo tissues were collected via previously described (Harrison et al. 1995). Briefly, female mice and male mice  were mated naturally, and the time when the vaginal plug was observed the next day was considered E0.5.


title: FAPs_240


title: FAPs_252


title: HMEC-1 cells, 50µM TMAO, 24H, 1


title: E65_ExE_mzKO_RNA_rep4


title: Th17 Scr 6h, rep1 [scRNA-seq]

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6 A

country: Finland

institute: Turku Bioscience Centre, University of Turku

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD4+ cells

extract_protocol:
Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10 X Genomics)
Chromium Single Cell Gene Expression Flex protocol (10 X Genomics)

value: CD4+ cells

value: scr


title: FAPs_239

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: FAPs_237


title: FAPs_238


title: E65_ExE_control_RNA_rep6

value: Tfap2c control


title: HMEC-1 cells, CTRL, 2


title: Th17 PIM TKD 6h, rep1 [scRNA-seq]

value: PIM TKD


title: FAPs_236


title: FAPs_245


title: PTKD_24h_rep4

data_processing:
The base calling was done using bcl2fastq
Read alignment was done using  Rsubread (v. 2.0.0)
Genewise read counts were calculated using Rsubread (v. 2.0.0)
Assembly: human genome hg38
Supplementary files format and content: genewise read counts for each sample.

source_name: Th17-polarized cells_PTKD_24h

extract_protocol:
RNeasy Mini Kit (Qiagen)
Illumina TruSeq® Stranded mRNA sample protocol

value: Th17-polarized cells


title: FAPs_235


title: E65_ExE_control_RNA_rep5


title: E65_ExE_control_RNA_rep4


title: FAPs_234


title: FAPs_233


title: Scr_24h_rep4

source_name: Th17-polarized cells_Scr_24h


title: E65_ExE_control_RNA_rep3


title: FAPs_232


title: FAPs_230


title: FAPs_231


title: PTKD_24h_rep3


title: E65_ExE_mzKO_RNA_rep1


title: FAPs_229


title: FAPs_226


title: FAPs_227


title: FAPs_228


title: PTKD_24h_rep2


title: E65_Epi_mzKO_RNA_rep9

source_name: E6.5 epiblast


title: E65_Epi_mzKO_RNA_rep8


title: FAPs_223


title: FAPs_224


title: FAPs_222


title: PTKD_24h_rep1


title: Scr_24h_rep2


title: FAPs_221


title: FAPs_225


title: E65_Epi_mzKO_RNA_rep10


title: Scr_24h_rep3


title: Scr_24h_rep1


title: FAPs_220


title: E65_Epi_mzKO_RNA_rep6


title: PTKD_6h_rep4

source_name: Th17-polarized cells_PTKD_6h


title: FAPs_218


title: FAPs_217


title: FAPs_219


title: Scr_6h_rep4

source_name: Th17-polarized cells_Scr_6h


title: FAPs_216


title: E65_Epi_mzKO_RNA_rep5


title: E65_Epi_mzKO_RNA_rep7


title: FAPs_215


title: FAPs_212


title: FAPs_210


title: FAPs_211


title: E65_Epi_control_RNA_rep4


title: PTKD_6h_rep2


title: FAPs_213


title: E65_Epi_control_RNA_rep5


title: Scr_6h_rep3


title: FAPs_209


title: E65_Epi_mzKO_RNA_rep4


title: Scr_6h_rep2


title: FAPs_207