title: AH1215_Calu3_BACH1 siRNA_CFTR -20.9 kb

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description:
4C-seq library with the CFTR +48.9 kb region as the viewpoint
AH1215

data_processing:
Library strategy: 4C-seq
Libraries ( AH1052, AH1054, AH1144, AH1147, AH1143, AH1146)  were sequenced on Illumina HiSeq4000 machine and others (AH1214, AH1215)  were sequenced on Illumina NextSeq550 machine.
Data were analyzed using 4cseq pipeline http://compgenomics.weizmann.ac.il/tanay/?page_id=367
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are a dataframe for each genomic fragment, together with its measured interaction frequency with the viewpoint of interest. The processed data can be used to plot a domainogram to visualize these interaction frequencies.

source_name: Human lung

growth_protocol: Cells were grown in indicated media using standard methods

extract_protocol:
Nuclei were made as per the above Methods papers with corresponding samples as listed in the treatment protocol section.
All libraries were constructed as per the above papers  PMID: 22609568 or PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per above papers  PMID: 22609568 or PMID: 31351925 for corresponding samples as listed in the tratement protocol section.

value: Human lung adenocarcinoma cell line

value: WT_BACH1 siRNA Knockdown

tag: growth media

value: DMEM + 10% FBS


title: AH1214_Calu3_NC siRNA_CFTR -20.9 kb

status: Public on Nov 17 2021

type: SRA

country: USA

description:
4C-seq library with the CFTR -20.9 kb region as the viewpoint
AH1214

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT_NC siRNA Knockdown


title: T3M3: FMN_WT_14d_rep4

type: RNA

city: Amsterdam

first: Matthew

last: Mason

address: Meibergdreef 47

department: Neuroregeneration

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Gene expression in cre-/Floxed Jun mouse facial nucleus, 14 days after facial nerve injury

hyb_protocol: Samples were hybridized to an Agilent Whole Mouse Genome Microarray 4x44K (catalog no. G4122F)  for 17 h at 65°C in a rotating hybridization chamber. Arrays were washed in 6 x saline sodium phosphate–EDTA (SSPE)/0.005% N-lauroylsarcosine (Sigma-Aldrich, St. Louis, MO, USA) for 5 min, then in 0.06 x SSPE/0.005% N-lauroylsarcosine for 1 min, and finally in acetonitrile (Sigma-Aldrich) for 30 sec, followed by drying in a nitrogen flow

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner at 5 mm resolution and 100% photomultiplier tube setting

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

molecule: total RNA

organism: Mus musculus

label_protocol: The Low Input Quick Amp Labeling Kit (Agilent Technologies) was used for sample amplification and fluorescent labeling. 200 ng RNA input was used.

extract_protocol: Total RNA was extracted using Trizol and Rneasy micro columns

treatment_protocol: The right facial nucleus of each animal  was dissected by cryosectioning followed by laser dissection microscopy.

tag: tissue

value: facial nucleus

value: cre-/Floxed Jun

tag: timepoint


title: T2M0: FMN_WT_4d_rep1

description: Gene expression in cre-/Floxed Jun mouse facial nucleus, 4 days after facial nerve injury

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M4: FMN_KO_14d_rep1

description: Gene expression in cre+/Floxed Jun mouse facial nucleus, 14 days after facial nerve injury

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

value: cre+/Floxed Jun


title: T2M3: FMN_WT_4d_rep4

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M6: FMN_KO_4d_rep5

description: Gene expression in cre+/Floxed Jun mouse facial nucleus, 4 days after facial nerve injury

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M1: FMN_WT_4d_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M7: FMN_KO_14d_rep4

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819466_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M9: FMN_WT_4d_rep6

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M8: FMN_WT_4d_rep5

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M1: FMN_WT_14d_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M6: FMN_KO_14d_rep3

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M5: FMN_KO_14d_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819466_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M8: FMN_WT_14d_rep5

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M2: FMN_WT_14d_rep3

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819466_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M2: FMN_WT_4d_rep3

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T3M0: FMN_WT_14d_rep1

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M5: FMN_KO_4d_rep4

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M7: FMN_KO_4d_rep6

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: 2NHV

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

library_source: transcriptomic

data_processing:
fastQC (v0.11.8) quality control
cutadapt (v2.3) adapter trimming and filtering
bowtie (v1.2.2) genome alignment
miRDeep2 (v2.0.1.2) miRNA quantification
edgeR (v3.28) differential expression
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: miRNA RPM matrix

source_name: Plasma

extract_protocol:
Maxwell RSC miRNA Tissue kit (Promega, AS1460)
RealSeq-Biofluids Plasma/Serum miRNA Library kit for Illumina sequencing (RealSeq Biosciences, 600-00048; protocol 20181220_RealSeq-BF_CL)

value: NHV

tag: group


title: T2M11: FMN_KO_4d_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M3: FMN_WT_1d_rep4

description: Gene expression in cre-/Floxed Jun mouse facial nucleus, 1 day after facial nerve injury

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M7: FMN_KO_1d_rep4

description: Gene expression in cre+/Floxed Jun mouse facial nucleus, 1 day after facial nerve injury

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819466_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M0: FMN_WT_1d_rep1

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M4: FMN_KO_1d_rep1

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M5: FMN_KO_1d_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M2: FMN_WT_1d_rep3

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819466_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M4: FMN_KO_4d_rep3

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M1: FMN_WT_1d_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T1M6: FMN_KO_1d_rep3

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T2M10: FMN_KO_4d_rep1

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T0M8: FMN_WT_uninjured_rep4

description: Gene expression in cre-/Floxed Jun mouse facial nucleus, uninjured

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

value: uninjured


title: Bovine mammary epithelial cells induced with LPS at 12 hpi [L_12h_1]

city: Yinchuan

first: Xing-Ping

last: Wang

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

country: China

institute: Ningxia University

data_processing:
Illumina PE150 used for basecalling.
The raw data containing a small number of reads with sequencing adapters or with low sequencing quality was obtained. In the step, reads with adapter were removed, unidentifiable base information reads with a ratio of > 0.002 were removed and the paired reads were removed when the number of low-mass bases in single-end read was more than 50% of the read length ratio. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The clean reads obtained during above process were mapped to the internal reference genome by using Hisat2. The lncRNAs were identified according to their structural and functional characteristics using the Cuffcompare software (v2.2.1). Meanwhile, circRNA were detected and identified using find_circ and CIRI2.
Differential expression analyses of lncRNA and circRNA between 2 groups were conducted using the Cuffdiff software (v2.1.1) and DESeq R package(1.10.1), respectively. The DElncRNAs were identified using |log2(FoldChange)| >1 and P < 0.05 as standard.In addition, DEcircRNAs were identified using |log2(Fold Change)| > 0.5 and P < 0.05 as standard.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with information of RNAs (lncRNA and circRNA) and expression level of RNAs (lncRNA was normalized using FPKM  and circRNA was normalized using TPM) for each sample.

organism: Bos taurus

source_name: bMECs induced with LPS at 12 hpi

growth_protocol: Bovine mammary epithelial cells (bMEC) previously frozen from our laboratory were cultured by DMEM/F12 in a 5% CO2  incubator. When bMEC monolayers reached 80% confluence, one 6-well plate cells (0 hpi) were collected as the control group, and the remaining two 6-well plates were treated with LPS to stimulate an inflammatory response

extract_protocol:
Total RNA was extracted from bovine mammary epithelial cells induced with LPS at 0, 6, and 12 hpi using TRizol reagent (Takara Biomedical Technology Co., Ltd, Beijing, China) according to the manufacturer’s instructions.
Ribosomal RNA was depleted with a Ribo-Zero rRNA removal kit (Epicenter, Madison, WI, USA) before constructing RNA-seq libraries. Preparation of the RNA sequencing library construction was prepared according to the product instruction, and then the library concentration was preliminarily tested using Qubit 2.0, and was adjusted to 1.0 ng/μL.

treatment_protocol: Bovine mammary epithelial cells were stimulated with 50 ng/μL LPS for 0, 6 and 12 h to product an inflamination response. All treatment groups had three biological replicates. Cells were collected at 0, 6 and 12 hpi, respectively, and stored at -80 °C for further analysis.

value: Bovine mammary epithelial cells (bMEC)

tag: treatment

value: 50 ng/μL LPS

tag: hpi

value: 12 hpi


title: Bovine mammary epithelial cells induced with LPS at 12 hpi [L_12h_3]


title: Bovine mammary epithelial cells induced with LPS at 6 hpi [L_6h_2]

source_name: bMECs induced with LPS at 6 hpi

value: 6 hpi


title: Bovine mammary epithelial cells induced with LPS at 0 hpi [L_0h_2]

source_name: bMECs induced with LPS at 0 hpi

value: 0 hpi


title: Bovine mammary epithelial cells induced with LPS at 6 hpi [L_6h_1]


title: Bovine mammary epithelial cells induced with LPS at 6 hpi [L_6h_3]


title: HCC1954 shSUFU-rep2

city: Dalian

first: dapeng

last: Liang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

data_processing:
Clean data were obtained by trimming adapter and low quality reads from raw fastq data using fastp with --length_required 50 and --detect_adapter_for_pe options
Clean reads were aligned to the hg38 genome assembly using STAR
STAR with --quantMode option was used to generate gene-level count matrix as input for DESeq2 statistical model
Convert Ensembl IDs to Entrez IDs and discard any unmapped features. Multimapped Ensembl IDs were also discarded to enforce unique mapping. Only features with unique Ensembl ID to Entrez ID mappings were retained.
Differential expression analysis between oeSUFU and oeControl (shSUFU and shControl ) cells was performed using DESeq2 package
Genome_build: hg38
Supplementary_files_format_and_content: csv file include gene raw count and gene annotation

source_name: HCC1954 cells

growth_protocol: SKBR3 cells were routinely generated by re-plating with 5A supplied with 10% FBS. HCC1954 cells were routinely generated by re-plating with 1640 supplied with 10% FBS.

extract_protocol:
RNA was isolated from SKBR3-oeSUFU/oeControl cells or HCC1954-shSUFU/shControl  using TRIzol Reagent.
The sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions.

treatment_protocol: SKBR3 cells were infected with pCDH-CTRL and SUFU-oeRNA lentiviruses. HCC1954 cells were infected with pGIPZ-CTRL and SUFU-shRNA lentiviruses. stable clones were selected using puromycin.

value: breast cancer epithelial cells

tag: shRNA

value: shSUFU

value: breast


title: HCC1954 shSUFU-rep1


title: Bovine mammary epithelial cells induced with LPS at 12 hpi [L_12h_2]


title: Bovine mammary epithelial cells induced with LPS at 0 hpi [L_0h_3]


title: Bovine mammary epithelial cells induced with LPS at 0 hpi [L_0h_1]


title: MoIug4-ChIP

city: Nanjing

first: Zhengguang

last: Zhang

address: Weigang No.1

institute: Nanjing agricultural university

data_processing:
Basecalls performed using Bowtie2
ChIP-seq reads were aligned to the Rice Genome Annotation Project
Data were filtered using the following specifications:Mismatches of no more than two bases, of which the only matched reads (the reads matched to the only position on the genome) will be used for subsequent information analysis
peaks were called using Macs2.Based on the sequence located on the genome and its abundance, we can find those statistically significant site peaks.
Genome_build: Rice Genome Annotation Project
Supplementary_files_format_and_content: bigWig

organism: Oryza sativa

source_name: rice leaves

growth_protocol: MoIug4-GFP overexpressed in rice

extract_protocol:
1. Rice leaves were prepared for 15 days and 1g  2. The harvested leaves were divided with one part being immediately frozen in liquid nitrogen for future RNA isolation and RNA-seq.  3. Cross-linking. Re-suspending ~3 g mycelia in 54 ml of Buffer A with 1% formaldehyde (~1.5 ml) in 125 ml flask for 10 min under shaking (160 rpm) at 28℃.  4. Stop cross-linking by adding 1.25 M glycine (final concentration 0.125 M), continue incubation for 5min.  5. Rinse the leaves with a lot of water to remove formaldehyde. Mycelia were collect and dry well.  6. Grind frozen leaves in a chilled (with LOTS of liquid N) mortar and pestle. Transfer fine powder to 20 ml cell lysis buffer and brief vortex. Stay on ice for 5 min. The following operations should keep on the ice.  7. Using four layers of filter cloth filter collecting the filtrate in a new 50 ml tube. Centrifuge at 1,350 g for 10 min at 4°C. This step is critical. Check sample by microscopy before centrifuging, make sure the filtrate contains free nuclei.   8. Discard supernatant and re-suspend pellet into 200-250ul of nuclei lysis buffer for 30 min. Keep cold.  9. DNA fragmentation. The sample should dilute 1 time with TE buffer (the concentration of SDS is 0.5%). The diluted samples sonicated with Biorupter in the following condition: 30 sec ON and 30 sec OFF at power level H for total 8 min. 4 samples were broken at one time, and the four samples were placed next to each other, each sample 100 ul.  Note: sonication is the most important step for ChIP. Conditions depend on type of sonicator. The ChIP DNA should shear to an average size of 250 bp ranging from 100-500bp.  10. Centrifuge at 12,000 rpm for 5 min at 4 °C.   11. Absorb supernatant, if proceeding to ChIP immdediately store on ice, otherwise put at -80°C immediately. 30 ul sample was divided into a new 1.5 ml tube for reverse crosslinking of the input control. The remaining sample was saved for immunoprecipitation.  Day2: Immunoprecipitation  12. The GFP-Trap® - ChromoTek was used to Immunoprecipitation, and 35 ul agarose bead for each tube. Add 1 ml of wash buffer, inverse 6 times, centrifuge at 2600 g for 3 min at 4°C, discard supernatant. Repeat one time and will be used.  13. The sample saved for immunoprecipitation was diluted 5 times again (the concentration of SDS is 0.1%). 1 ml dilution sample was added to the tube with 30 ml beads. Rotate at 4°C for 2 hours.   14. Centrifuge at 2600 g for 3min at 4°C, discard supernatant.  15. Add 1 ml of wash buffer, inverse 6 times, centrifuge at 2600 g for 3min at 4°C, pipet off supernatant. Repeat two times.  16. Add 50 ul glycine and gently beat tube for 1 min. the sample should be in cold.  17. Transfer 45 ul supernatant to a new tube and add 5 ul Tris-base - this is your ChIP’d DNA.  18. Add 5.5 ul of 2 M NaCl (the concentration of NaCl is 0.2 M) and incubate ovetnight at 65°C for reverse crosslinging. From this step, he input sample and ChIP’d DNA have same treatments.   Day 3: Prurify ChIPed DNA  19. Add 1 ul of RNase A and incubate for 30 min at 37°C.  20. Add 2 ul of Proteinase K and incubate for 90 min at 42°C.  21. Add 120 ul of EtOH at -20°C for 30 min to precipitation. Centrifuge at 12,000 rpm for 10 min and dry.  22. Add 25 ul ddH2O at 37°C for 30 min. This is the final ChIP’d DNA and is named output.  23. The input and output send to company for sequencing.
prepared for sequencing using standard Illumina protocols

treatment_protocol: without treatment

value: leaves

tag: antibody


title: HCC1954 shControl-rep2

value: shControl


title: SKBR3 oeSUFU-rep2

source_name: SKBR3 cells

value: oeSUFU


title: HCC1954 shControl-rep1


title: SKBR3 oeControl-rep1

value: oeControl


title: SKBR3 oeControl-rep2


title: T0M6: FMN_KO_uninjured_rep3 (2 tech. reps)

description: Gene expression in cre+/Floxed Jun mouse facial nucleus, uninjured

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819466_S01_GE2-v5_95_Feb07_1_4.txt

raw data corresponds to Cy5 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

value: facial nucleus


title: T0M2: FMN_WT_uninjured_rep3 (2 tech. reps)

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819526_S01_GE2-v5_95_Feb07_1_4.txt

raw data corresponds to Cy3 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_3.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

value: cre-/Floxed Jun


title: T0M0: FMN_WT_uninjured_rep1

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_1.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T0M5: FMN_KO_uninjured_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819470_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

value: cre+/Floxed Jun


title: T0M3: FMN_KO_uninjured_rep1

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_4.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T0M1: FMN_WT_uninjured_rep2

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy5 channel of file:
US12302316_251486819467_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: T0M7: FMN_KO_uninjured_rep4

data_processing:
Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA. Where 2 entries appear above for one sample, these are technical replicates.

raw data corresponds to Cy3 channel of file:
US12302316_251486819957_S01_GE2-v5_95_Feb07_1_2.txt

rejected for technical failure: Cy5 channel of
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt


title: MCF7 siRNA NDP52 3

city: Sheffield

first: Chris

last: Toseland

address: Medical School

country: United Kingdom

institute: University of Sheffield

description: siRNA NDP52 3

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: GRch38
Supplementary_files_format_and_content: Tab-delimited text files (TSV) include read counts for each sample.

source_name: MCF7 cells

growth_protocol: Full DMEM medium with 10%FBS and Pen/Strep

extract_protocol:
Total RNA was extracted from three replicates of NDP52 KD (using CALCOCO2 siRNA, Ambion, 4392420) and scrambled siRNA (using control siRNA, Qiagen, 1027280) in MCF-7 cells. Ice cold TRIzol reagent was added to each cell culture dish and homogenised. The mixture was incubated at room temperature for 10 minutes. Chloroform was then added to the mixture and incubated at room temperature for 5 minutes. The samples were centrifuged at 8,000 xg. The top, aqueous layer was collected and isopropanol was added. The mixture was then centrifuged at 12, 000 xg for 30 minutes and the supernatant discarded. The pellet was washed in 75% (v/v) ethanol and centrifuged at 7, 500 xg for 5 minutes. The pellet was air dried and resuspended in RNAse-free H2O. RNA concentration and quality was then assessed by measuring absorbance at 260 nm and A260/A280 ratio. RNA samples were stored at -80°C. The following procedures were performed by  Glasgow Polyomics. The RNA-seq libraries were prepared using Poly-A selection. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer and on an Agilent 2100 bioanalyzer. Paired-end sequencing was then performed on an (2x75 bp) on a HiSeq sequencer  (Glasgow Polyomics).
The following procedures were performed by Glasgow Polyomics. The RNA-seq libraries were prepared using Poly-A selection. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer and on an Agilent 2100 bioanalyzer.

treatment_protocol: For NDP52 KD experiments, MCF7 cell monolayers were seeded at 50% confluency and then transfected with NDP52 KD (using CALCOCO2 siRNA, Ambion, 4392420) or scrambled siRNA (using control siRNA, Qiagen, 1027280) using lipofectamine 2000. Cells were harvested at 48hrs.

value: mammary epithelium


title: MCF7 siRNA NDP52 2

description: siRNA NDP52 2


title: MCF7 WT control 3

description: WT control 3


title: MCF7 siRNA NDP52 1

description: siRNA NDP52 1


title: MCF7 WT Control 1

description: WT Control 1


title: MCF7 WT Control 2

description: WT Control 2


title: RNA-seq in shMMP9 A375 rep1

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
For RNA-seq, reads were mapped to hg38 GENCODE version 29 using STAR 2.6.1d and aligned reads were quantified at the gene level using Partek® Flow® software Quantify to annotation model  (Partek Inc., St. Louis, MO, USA). Dfferentially expressed genes between shControl and shMMP9 groups were selected by using the Gene Specific Algorithm from Partek® Flow® software using the upper quartile normalization method (Partek Inc., St. Louis, MO, USA).
Genome_build: hg38
Supplementary_files_format_and_content: Gene count txt file includes log2(Upper Quartile+1) gene expression levels for all samples

source_name: Human malignant melanoma cell line A375

growth_protocol: A375 cells were cultured in Dulbecco’s modiﬁed Eagle’s medium containing 10% fetal bovine serum.

extract_protocol:
RNA was prepared from mock- or MMP-9-depleted A375 cells using the Qiagen RNeasy kit (Qiagen, CA) according to the manufacturer’s instructions
The library preparation were done as described (Kim et al., 2016).

treatment_protocol: DNA oligonucleotides encoding shRNAs speciﬁc for MMP-9 (5’-CATTCAGGGAGACGCCCATTT-3’) coding regions were annealed and ligated into the lentiviral expression vector pLKO.1 (Addgene, USA). Lentiviral particles were generated in 293T cells by transfecting plasmids encoding VSV-G, NL-BH, and the shRNAs. Two days after transfection, the soups containing the viruses were collected and used to infect A375 in the presence of polybrene (8 μg/ml). The cell lines were selected for two weeks in the presence of puromycin (2 μg/ml).


title: RNA-seq in shCtrl A375 rep2


title: RNA-seq in shMMP9 A375 rep3


title: RNA-seq in shMMP9 A375 rep2


title: Donor 4, yd(T2) Day 15

city: London

first: John

last: Maher

address: Great Maze Pond

institute: King's College London

data_processing:
The quality of the sequencing tags was inspected with fastQC.
Raw reads were trimmed and filtered to remove adaptor contamination and poor-quality bases using trimmomatic (Bolger et al., 2014).
The resulting read files were mapped to the GRCh38 assembly of the human genome using Hisat2 with default parameters (Kim et al., 2015).
The number of reads mapping to the genomic features annotated in Ensembl (Yates et al., 2020) with a MAPQ score higher than or equal to 30 was calculated for all samples using htseq-count with default parameters (Anders et al., 2015).
Genome_build: GRCh38
Supplementary_files_format_and_content: one tab-delimited text file for each sample with the Hisat2 output raw counts

molecule: polyA RNA

source_name: Vy9Vd2 cells expanded with zoledronate and IL-2 and TGFbeta1

growth_protocol: PBMCs from healthy volunteers were cultured in TexMACs (serum-free) media supplemented with GlutaMax at 37C 5% CO2 for 9 or 15 days.

extract_protocol:
Cells were harvested, stained with an anti-yd TCR antibody and FACS sorted (BD FACSAria II Cell Sorter) for live yd TCR cells. Total RNA was isolated from the sorted live cells using TRIzol. Ribosomal RNA was removed using Ribo-Zero.
PolyA isolation and library preparation were performed using NEBNext and the sample were run on Illumina HISeq platform.

treatment_protocol: PBMCs were treated with 1ug/ml zoledronate and 100U/ml IL-2. yd(T2) cells were additonally treated with 5ng/ml TGFbeta1. Cytokines were replenished every 3 days.

tag: source tissue

value: Healthy volunteer PBMCs

tag: days of treatment

value: zoledronate and IL-2 and TGFbeta1


title: Donor 1, yd(T2) Day 15


title: Donor 3, yd(2) Day 15

source_name: Vy9Vd2 cells expanded with zoledronate and IL-2

value: zoledronate and IL-2


title: RNA-seq in shCtrl A375 rep3


title: SKBR3 oeSUFU-rep1


title: Donor 3, yd(T2) Day 15


title: Donor 1, yd(2) Day 15


title: Donor 4, yd(T2) Day 9


title: Donor 4, yd(2) Day 9


title: Donor 3, yd(T2) Day 9


title: Sample LS174T-2D-3 technical replicate h

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: LS174T cell line 2D layer growth, sample 3 technical replicate h

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.3. Before mapping, adapters were removed using Trim Galore! (version 0.4.1), poly N read tail were trimmed, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Homoe sapiens genome (hg19 genome assembly from Ensembl version 91) using the STAR mapper (version 2.6.1b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Homo sapiens GTF genome annotation from from Ensembl version 91. All overlapping regions between alignments and referenced exons were counted and aggregated by genes with HTSeq-count 0.5.3.
Genome_build: Hg19 version Ensembl 91
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: Colorectal cancer cell line

extract_protocol:
Total RNA were extracted from the four CRC cell lines grown in either 2D or 3D conditions by using the RNeasy® Plus Micro Kit (Qiagen), as described by the supplier.
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

value: LS174T cell line

tag: growth

value: 2D growth


title: Donor 3, yd(2) Day 9


title: Sample LS174T-2D-3 technical replicate e

description: LS174T cell line 2D layer growth, sample 3 technical replicate e


title: RNA-seq in shCtrl A375 rep1


title: Sample LS174T-2D-3 technical replicate g

description: LS174T cell line 2D layer growth, sample 3 technical replicate g


title: Sample LS174T-2D-3 technical replicate f

description: LS174T cell line 2D layer growth, sample 3 technical replicate f


title: Donor 1, yd(2) Day 9


title: Donor 1, yd(T2) Day 9


title: Sample LS174T-2D-3 technical replicate d

description: LS174T cell line 2D layer growth, sample 3 technical replicate d


title: Donor 4, yd(2) Day 15


title: Sample LS174T-2D-3 technical replicate c

description: LS174T cell line 2D layer growth, sample 3 technical replicate c


title: Sample LS174T-2D-2 technical replicate g

description: LS174T cell line 2D layer growth, sample 2 technical replicate g


title: Sample LS174T-2D-3 technical replicate a

description: LS174T cell line 2D layer growth, sample 3 technical replicate a


title: Sample LS174T-2D-2 technical replicate e

description: LS174T cell line 2D layer growth, sample 2 technical replicate e


title: Sample LS174T-2D-2 technical replicate c

description: LS174T cell line 2D layer growth, sample 2 technical replicate c


title: Sample LS174T-2D-2 technical replicate f

description: LS174T cell line 2D layer growth, sample 2 technical replicate f


title: Sample LS174T-2D-2 technical replicate h

description: LS174T cell line 2D layer growth, sample 2 technical replicate h


title: Sample LS174T-2D-1 technical replicate g

description: LS174T cell line 2D layer growth, sample 1 technical replicate g


title: Sample LS174T-2D-1 technical replicate f

description: LS174T cell line 2D layer growth, sample 1 technical replicate f


title: Sample LS174T-2D-2 technical replicate b

description: LS174T cell line 2D layer growth, sample 2 technical replicate b


title: Sample LS174T-2D-2 technical replicate a

description: LS174T cell line 2D layer growth, sample 2 technical replicate a


title: Sample LS174T-2D-1 technical replicate e

description: LS174T cell line 2D layer growth, sample 1 technical replicate e


title: Sample LS174T-2D-1 technical replicate d

description: LS174T cell line 2D layer growth, sample 1 technical replicate d


title: Sample LS174T-2D-1 technical replicate c

description: LS174T cell line 2D layer growth, sample 1 technical replicate c


title: Sample LS174T-2D-1 technical replicate b

description: LS174T cell line 2D layer growth, sample 1 technical replicate b


title: Sample LS513-2D-3 technical replicate g

description: LS513 cell line 2D layer growth, sample 3 technical replicate g

value: LS513 cell line


title: Sample LS513-2D-3 technical replicate f

description: LS513 cell line 2D layer growth, sample 3 technical replicate f


title: Sample LS174T-2D-1 technical replicate a

description: LS174T cell line 2D layer growth, sample 1 technical replicate a


title: Sample LS513-2D-3 technical replicate d

description: LS513 cell line 2D layer growth, sample 3 technical replicate d


title: Sample LS174T-2D-3 technical replicate b

description: LS174T cell line 2D layer growth, sample 3 technical replicate b


title: Sample LS513-2D-3 technical replicate c

description: LS513 cell line 2D layer growth, sample 3 technical replicate c


title: Sample LS513-2D-2 technical replicate h

description: LS513 cell line 2D layer growth, sample 2 technical replicate h


title: Sample LS174T-2D-2 technical replicate d

description: LS174T cell line 2D layer growth, sample 2 technical replicate d


title: Sample LS513-2D-2 technical replicate f

description: LS513 cell line 2D layer growth, sample 2 technical replicate f


title: Sample LS513-2D-3 technical replicate a

description: LS513 cell line 2D layer growth, sample 3 technical replicate a


title: Sample LS513-2D-2 technical replicate e

description: LS513 cell line 2D layer growth, sample 2 technical replicate e


title: Sample LS174T-2D-1 technical replicate h

description: LS174T cell line 2D layer growth, sample 1 technical replicate h


title: Sample LS513-2D-2 technical replicate g

description: LS513 cell line 2D layer growth, sample 2 technical replicate g


title: Sample LS513-2D-2 technical replicate c

description: LS513 cell line 2D layer growth, sample 2 technical replicate c


title: Sample LS513-2D-2 technical replicate a

description: LS513 cell line 2D layer growth, sample 2 technical replicate a


title: Sample LS513-2D-1 technical replicate g

description: LS513 cell line 2D layer growth, sample 1 technical replicate g


title: Sample LS513-2D-2 technical replicate d

description: LS513 cell line 2D layer growth, sample 2 technical replicate d


title: Sample LS513-2D-1 technical replicate e

description: LS513 cell line 2D layer growth, sample 1 technical replicate e


title: Sample LS513-2D-1 technical replicate h

description: LS513 cell line 2D layer growth, sample 1 technical replicate h


title: Sample LS513-2D-1 technical replicate f

description: LS513 cell line 2D layer growth, sample 1 technical replicate f


title: Sample LS513-2D-3 technical replicate h

description: LS513 cell line 2D layer growth, sample 3 technical replicate h


title: Sample LS513-2D-1 technical replicate a

description: LS513 cell line 2D layer growth, sample 1 technical replicate a


title: Sample LS513-2D-1 technical replicate b

description: LS513 cell line 2D layer growth, sample 1 technical replicate b


title: Sample LS513-2D-1 technical replicate d

description: LS513 cell line 2D layer growth, sample 1 technical replicate d


title: Sample LS513-2D-3 technical replicate e

description: LS513 cell line 2D layer growth, sample 3 technical replicate e


title: Sample LS513-2D-3 technical replicate b

description: LS513 cell line 2D layer growth, sample 3 technical replicate b


title: Sample HCT116-2D-3 technical replicate h

description: HCT116 cell line 2D layer growth, sample 3 technical replicate h

value: HCT116 cell line


title: Sample HCT116-2D-3 technical replicate g

description: HCT116 cell line 2D layer growth, sample 3 technical replicate g


title: Sample HCT116-2D-3 technical replicate f

description: HCT116 cell line 2D layer growth, sample 3 technical replicate f


title: Sample HCT116-2D-3 technical replicate d

description: HCT116 cell line 2D layer growth, sample 3 technical replicate d


title: Sample HCT116-2D-3 technical replicate c

description: HCT116 cell line 2D layer growth, sample 3 technical replicate c


title: Sample HCT116-2D-2 technical replicate h

description: HCT116 cell line 2D layer growth, sample 2 technical replicate h


title: Sample HCT116-2D-3 technical replicate b

description: HCT116 cell line 2D layer growth, sample 3 technical replicate b


title: Sample HCT116-2D-3 technical replicate a

description: HCT116 cell line 2D layer growth, sample 3 technical replicate a


title: Sample LS513-2D-2 technical replicate b

description: LS513 cell line 2D layer growth, sample 2 technical replicate b


title: Sample LS513-2D-1 technical replicate c

description: LS513 cell line 2D layer growth, sample 1 technical replicate c


title: Sample HCT116-2D-2 technical replicate d

description: HCT116 cell line 2D layer growth, sample 2 technical replicate d


title: Sample HCT116-2D-2 technical replicate f

description: HCT116 cell line 2D layer growth, sample 2 technical replicate f


title: Sample HCT116-2D-2 technical replicate b

description: HCT116 cell line 2D layer growth, sample 2 technical replicate b


title: Sample HCT116-2D-2 technical replicate a

description: HCT116 cell line 2D layer growth, sample 2 technical replicate a


title: Sample HCT116-2D-2 technical replicate c

description: HCT116 cell line 2D layer growth, sample 2 technical replicate c


title: Sample HCT116-2D-2 technical replicate g

description: HCT116 cell line 2D layer growth, sample 2 technical replicate g


title: Sample HCT116-2D-1 technical replicate f

description: HCT116 cell line 2D layer growth, sample 1 technical replicate f


title: Sample HCT116-2D-1 technical replicate e

description: HCT116 cell line 2D layer growth, sample 1 technical replicate e


title: Sample HCT116-2D-1 technical replicate h

description: HCT116 cell line 2D layer growth, sample 1 technical replicate h


title: Sample HCT116-2D-1 technical replicate a

description: HCT116 cell line 2D layer growth, sample 1 technical replicate a


title: Sample HCT116-2D-1 technical replicate b

description: HCT116 cell line 2D layer growth, sample 1 technical replicate b


title: Sample HCT116-2D-1 technical replicate c

description: HCT116 cell line 2D layer growth, sample 1 technical replicate c


title: Sample HCT116-2D-3 technical replicate e

description: HCT116 cell line 2D layer growth, sample 3 technical replicate e


title: Sample HT29-2D-3 technical replicate g

description: HT29 cell line 2D layer growth, sample 3 technical replicate g

value: HT29 cell line


title: Sample HT29-2D-3 technical replicate h

description: HT29 cell line 2D layer growth, sample 3 technical replicate h


title: Sample HT29-2D-3 technical replicate f

description: HT29 cell line 2D layer growth, sample 3 technical replicate f


title: Sample HT29-2D-3 technical replicate e

description: HT29 cell line 2D layer growth, sample 3 technical replicate e


title: Sample HT29-2D-3 technical replicate c

description: HT29 cell line 2D layer growth, sample 3 technical replicate c


title: Sample HT29-2D-3 technical replicate b

description: HT29 cell line 2D layer growth, sample 3 technical replicate b


title: Sample HT29-2D-3 technical replicate a

description: HT29 cell line 2D layer growth, sample 3 technical replicate a


title: Sample HT29-2D-2 technical replicate g

description: HT29 cell line 2D layer growth, sample 2 technical replicate g


title: Sample HT29-2D-2 technical replicate e

description: HT29 cell line 2D layer growth, sample 2 technical replicate e


title: Sample HCT116-2D-2 technical replicate e

description: HCT116 cell line 2D layer growth, sample 2 technical replicate e


title: Sample HT29-2D-2 technical replicate f

description: HT29 cell line 2D layer growth, sample 2 technical replicate f


title: Sample HT29-2D-2 technical replicate d

description: HT29 cell line 2D layer growth, sample 2 technical replicate d


title: Sample HT29-2D-2 technical replicate h

description: HT29 cell line 2D layer growth, sample 2 technical replicate h


title: Sample HCT116-2D-1 technical replicate g

description: HCT116 cell line 2D layer growth, sample 1 technical replicate g


title: Sample HCT116-2D-1 technical replicate d

description: HCT116 cell line 2D layer growth, sample 1 technical replicate d


title: Sample HT29-2D-2 technical replicate c

description: HT29 cell line 2D layer growth, sample 2 technical replicate c


title: Sample HT29-2D-1 technical replicate h

description: HT29 cell line 2D layer growth, sample 1 technical replicate h


title: Sample HT29-2D-2 technical replicate b

description: HT29 cell line 2D layer growth, sample 2 technical replicate b


title: Sample HT29-2D-1 technical replicate f

description: HT29 cell line 2D layer growth, sample 1 technical replicate f


title: Sample HT29-2D-2 technical replicate a

description: HT29 cell line 2D layer growth, sample 2 technical replicate a


title: Sample HT29-2D-1 technical replicate a

description: HT29 cell line 2D layer growth, sample 1 technical replicate a


title: Sample HT29-2D-1 technical replicate e

description: HT29 cell line 2D layer growth, sample 1 technical replicate e


title: Sample HT29-2D-1 technical replicate g

description: HT29 cell line 2D layer growth, sample 1 technical replicate g


title: Sample LS174T-3D-3 technical replicate e

description: LS174T cell line 3D layer growth, sample 3 technical replicate e

value: 3D growth


title: Sample HT29-2D-1 technical replicate d

description: HT29 cell line 2D layer growth, sample 1 technical replicate d


title: Sample LS174T-3D-3 technical replicate c

description: LS174T cell line 3D layer growth, sample 3 technical replicate c


title: Sample LS174T-3D-2 technical replicate h

description: LS174T cell line 3D layer growth, sample 2 technical replicate h


title: Sample HT29-2D-1 technical replicate b

description: HT29 cell line 2D layer growth, sample 1 technical replicate b


title: Sample HT29-2D-1 technical replicate c

description: HT29 cell line 2D layer growth, sample 1 technical replicate c


title: Sample LS174T-3D-3 technical replicate h

description: LS174T cell line 3D layer growth, sample 3 technical replicate h


title: Sample LS174T-3D-3 technical replicate f

description: LS174T cell line 3D layer growth, sample 3 technical replicate f


title: Sample LS174T-3D-3 technical replicate b

description: LS174T cell line 3D layer growth, sample 3 technical replicate b


title: Sample LS174T-3D-2 technical replicate g

description: LS174T cell line 3D layer growth, sample 2 technical replicate g


title: Sample LS174T-3D-3 technical replicate a

description: LS174T cell line 3D layer growth, sample 3 technical replicate a


title: Sample LS174T-3D-3 technical replicate g

description: LS174T cell line 3D layer growth, sample 3 technical replicate g


title: Sample HT29-2D-3 technical replicate d

description: HT29 cell line 2D layer growth, sample 3 technical replicate d


title: Sample LS174T-3D-2 technical replicate e

description: LS174T cell line 3D layer growth, sample 2 technical replicate e


title: Sample LS174T-3D-3 technical replicate d

description: LS174T cell line 3D layer growth, sample 3 technical replicate d


title: Sample LS174T-3D-2 technical replicate f

description: LS174T cell line 3D layer growth, sample 2 technical replicate f


title: Sample LS174T-3D-2 technical replicate d

description: LS174T cell line 3D layer growth, sample 2 technical replicate d


title: Sample LS174T-3D-2 technical replicate c

description: LS174T cell line 3D layer growth, sample 2 technical replicate c


title: Sample LS174T-3D-1 technical replicate h

description: LS174T cell line 3D layer growth, sample 1 technical replicate h


title: Sample LS174T-3D-1 technical replicate d

description: LS174T cell line 3D layer growth, sample 1 technical replicate d


title: Sample LS174T-3D-2 technical replicate b

description: LS174T cell line 3D layer growth, sample 2 technical replicate b


title: Sample LS174T-3D-1 technical replicate b

description: LS174T cell line 3D layer growth, sample 1 technical replicate b


title: Sample LS174T-3D-2 technical replicate a

description: LS174T cell line 3D layer growth, sample 2 technical replicate a


title: Sample LS174T-3D-1 technical replicate g

description: LS174T cell line 3D layer growth, sample 1 technical replicate g


title: Sample LS174T-3D-1 technical replicate f

description: LS174T cell line 3D layer growth, sample 1 technical replicate f


title: Sample LS174T-3D-1 technical replicate c

description: LS174T cell line 3D layer growth, sample 1 technical replicate c


title: Sample LS513-3D-3 technical replicate h

description: LS513 cell line 3D layer growth, sample 3 technical replicate h


title: Sample LS513-3D-3 technical replicate g

description: LS513 cell line 3D layer growth, sample 3 technical replicate g


title: Sample LS174T-3D-1 technical replicate e

description: LS174T cell line 3D layer growth, sample 1 technical replicate e


title: Sample LS513-3D-3 technical replicate e

description: LS513 cell line 3D layer growth, sample 3 technical replicate e


title: Sample LS174T-3D-1 technical replicate a

description: LS174T cell line 3D layer growth, sample 1 technical replicate a


title: Sample LS513-3D-3 technical replicate d

description: LS513 cell line 3D layer growth, sample 3 technical replicate d


title: Sample LS513-3D-3 technical replicate c

description: LS513 cell line 3D layer growth, sample 3 technical replicate c


title: Sample LS513-3D-2 technical replicate f

description: LS513 cell line 3D layer growth, sample 2 technical replicate f


title: Sample LS513-3D-2 technical replicate h

description: LS513 cell line 3D layer growth, sample 2 technical replicate h


title: Sample LS513-3D-2 technical replicate g

description: LS513 cell line 3D layer growth, sample 2 technical replicate g


title: Sample LS513-3D-3 technical replicate a

description: LS513 cell line 3D layer growth, sample 3 technical replicate a


title: Sample LS513-3D-3 technical replicate b

description: LS513 cell line 3D layer growth, sample 3 technical replicate b


title: Sample LS513-3D-2 technical replicate a

description: LS513 cell line 3D layer growth, sample 2 technical replicate a


title: Sample LS513-3D-2 technical replicate c

description: LS513 cell line 3D layer growth, sample 2 technical replicate c


title: Sample LS513-3D-2 technical replicate d

description: LS513 cell line 3D layer growth, sample 2 technical replicate d


title: Sample LS513-3D-2 technical replicate b

description: LS513 cell line 3D layer growth, sample 2 technical replicate b


title: Sample LS513-3D-2 technical replicate e

description: LS513 cell line 3D layer growth, sample 2 technical replicate e


title: Sample LS513-3D-1 technical replicate g

description: LS513 cell line 3D layer growth, sample 1 technical replicate g


title: Sample LS513-3D-1 technical replicate f

description: LS513 cell line 3D layer growth, sample 1 technical replicate f


title: Sample LS513-3D-1 technical replicate h

description: LS513 cell line 3D layer growth, sample 1 technical replicate h


title: Sample LS513-3D-1 technical replicate d

description: LS513 cell line 3D layer growth, sample 1 technical replicate d


title: Sample LS513-3D-1 technical replicate e

description: LS513 cell line 3D layer growth, sample 1 technical replicate e


title: Sample LS513-3D-3 technical replicate f

description: LS513 cell line 3D layer growth, sample 3 technical replicate f


title: Sample LS513-3D-1 technical replicate b

description: LS513 cell line 3D layer growth, sample 1 technical replicate b


title: Sample HCT116-3D-3 technical replicate h

description: HCT116 cell line 3D layer growth, sample 3 technical replicate h


title: Sample LS513-3D-1 technical replicate c

description: LS513 cell line 3D layer growth, sample 1 technical replicate c


title: Sample HCT116-3D-3 technical replicate g

description: HCT116 cell line 3D layer growth, sample 3 technical replicate g


title: Sample LS513-3D-1 technical replicate a

description: LS513 cell line 3D layer growth, sample 1 technical replicate a


title: Sample HCT116-3D-3 technical replicate d

description: HCT116 cell line 3D layer growth, sample 3 technical replicate d


title: Sample HCT116-3D-3 technical replicate f

description: HCT116 cell line 3D layer growth, sample 3 technical replicate f


title: Sample HCT116-3D-3 technical replicate c

description: HCT116 cell line 3D layer growth, sample 3 technical replicate c


title: Sample HCT116-3D-3 technical replicate b

description: HCT116 cell line 3D layer growth, sample 3 technical replicate b


title: Sample HCT116-3D-3 technical replicate e

description: HCT116 cell line 3D layer growth, sample 3 technical replicate e


title: Sample HCT116-3D-2 technical replicate h

description: HCT116 cell line 3D layer growth, sample 2 technical replicate h


title: Sample HCT116-3D-3 technical replicate a

description: HCT116 cell line 3D layer growth, sample 3 technical replicate a


title: Sample HCT116-3D-2 technical replicate g

description: HCT116 cell line 3D layer growth, sample 2 technical replicate g


title: Sample HCT116-3D-2 technical replicate c

description: HCT116 cell line 3D layer growth, sample 2 technical replicate c


title: Sample HCT116-3D-2 technical replicate d

description: HCT116 cell line 3D layer growth, sample 2 technical replicate d


title: Sample HCT116-3D-2 technical replicate e

description: HCT116 cell line 3D layer growth, sample 2 technical replicate e


title: Sample HCT116-3D-2 technical replicate f

description: HCT116 cell line 3D layer growth, sample 2 technical replicate f


title: Sample HCT116-3D-1 technical replicate e

description: HCT116 cell line 3D layer growth, sample 1 technical replicate e


title: Sample HCT116-3D-1 technical replicate h

description: HCT116 cell line 3D layer growth, sample 1 technical replicate h


title: Sample HCT116-3D-1 technical replicate b

description: HCT116 cell line 3D layer growth, sample 1 technical replicate b


title: Sample HCT116-3D-1 technical replicate a

description: HCT116 cell line 3D layer growth, sample 1 technical replicate a


title: Sample HT29-3D-4 technical replicate h

description: HT29 cell line 3D layer growth, sample 4 technical replicate h


title: Sample HT29-3D-4 technical replicate g

description: HT29 cell line 3D layer growth, sample 4 technical replicate g


title: Sample HT29-3D-4 technical replicate f

description: HT29 cell line 3D layer growth, sample 4 technical replicate f


title: Sample HT29-3D-4 technical replicate e

description: HT29 cell line 3D layer growth, sample 4 technical replicate e


title: Sample HT29-3D-4 technical replicate d

description: HT29 cell line 3D layer growth, sample 4 technical replicate d


title: Sample HT29-3D-4 technical replicate c

description: HT29 cell line 3D layer growth, sample 4 technical replicate c


title: Sample HT29-3D-4 technical replicate a

description: HT29 cell line 3D layer growth, sample 4 technical replicate a


title: Sample HT29-3D-4 technical replicate b

description: HT29 cell line 3D layer growth, sample 4 technical replicate b


title: Sample HT29-3D-3 technical replicate h

description: HT29 cell line 3D layer growth, sample 3 technical replicate h


title: Sample HT29-3D-3 technical replicate g

description: HT29 cell line 3D layer growth, sample 3 technical replicate g


title: Sample HT29-3D-3 technical replicate d

description: HT29 cell line 3D layer growth, sample 3 technical replicate d


title: Sample HT29-3D-3 technical replicate e

description: HT29 cell line 3D layer growth, sample 3 technical replicate e


title: Sample HCT116-3D-1 technical replicate g

description: HCT116 cell line 3D layer growth, sample 1 technical replicate g


title: Sample HCT116-3D-2 technical replicate b

description: HCT116 cell line 3D layer growth, sample 2 technical replicate b


title: Sample HT29-3D-3 technical replicate b

description: HT29 cell line 3D layer growth, sample 3 technical replicate b


title: Sample HCT116-3D-2 technical replicate a

description: HCT116 cell line 3D layer growth, sample 2 technical replicate a


title: Sample HCT116-3D-1 technical replicate f

description: HCT116 cell line 3D layer growth, sample 1 technical replicate f


title: Sample HCT116-3D-1 technical replicate d

description: HCT116 cell line 3D layer growth, sample 1 technical replicate d


title: Sample HT29-3D-3 technical replicate a

description: HT29 cell line 3D layer growth, sample 3 technical replicate a


title: Sample HT29-3D-3 technical replicate f

description: HT29 cell line 3D layer growth, sample 3 technical replicate f


title: Sample HCT116-3D-1 technical replicate c

description: HCT116 cell line 3D layer growth, sample 1 technical replicate c


title: Sample HT29-3D-1 technical replicate g

description: HT29 cell line 3D layer growth, sample 1 technical replicate g


title: Sample HT29-3D-1 technical replicate h

description: HT29 cell line 3D layer growth, sample 1 technical replicate h


title: Sample HT29-3D-1 technical replicate e

description: HT29 cell line 3D layer growth, sample 1 technical replicate e


title: Sample HT29-3D-1 technical replicate a

description: HT29 cell line 3D layer growth, sample 1 technical replicate a


title: Sample HT29-3D-1 technical replicate b

description: HT29 cell line 3D layer growth, sample 1 technical replicate b


title: Sample HT29-3D-1 technical replicate d

description: HT29 cell line 3D layer growth, sample 1 technical replicate d


title: HCT116 cells, siDDX41_rep2

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

data_processing:
Library strategy: BLISS-seq
Reads were mapped to the human genome (GRCh38/hg38) using BWA-MEM and only reads with mapping quality scores greater than 30 were retained.
PCR duplicates were filtered out by searching for proximal reads with at most two mismatches in the UMI sequence.
Bed files were generated containing a list of double-strand break (DSB) genomic locations associated with the number of unique UMIs identified.
BEDtools suite was used to generate bigwig files from bed files. First, one entry was created per UMI-DSB in the BED file and then each UMI-DSB was extended +/- 100bp.
Genome_build: hg38
Supplementary_files_format_and_content: bed files containing a list of genomic locations associated with unique UMIs. BigWig files were generated using BEDtools suite.

extract_protocol:
Fixed cells were lysed with mild buffers for nuclei extraction. After DSB blunting and A-tailing, BLISS adapters containing a T-overhang were ligated DSB ends. DNA was extracted using a SDS-based buffer and proteinase K, followed by phenol/chloroform extraction and ethanol precipitation.
After DNA sonication, the ligated DSB ends were linearly amplified using an in vitro transcription. The generated RNA was subject to a 3' ligation using a truncated RNA ligase 2, followed by a reverse transcription and PCR amplification with barcoded primers (Bouwman et al., 2020 - Nature Protocols).

value: colorectal carcinoma cells

value: siRNA knockdown of DDX41


title: HCT116 cells, siDDX41_rep1


title: U2OS cells, DDX41_crosslink_rep1

data_processing:
Base calling was performed with RTA v.2.4.11  and and demultiplexing was done using bcl2fastq v.2.19.1
The data was trimmed for sequencing adapters and the first 15 bases of read 2 were removed (added during library construction).
Mapping was done against hg38 using bowtie2 (v. 2.3.4). Multi mapping reads were excluded from further analysis.
Sequencing depth normalized coverage tracks were created using Deeptools (v3.4.1). chrM was excluded from the normalization
Genome_build: hg38
Supplementary_files_format_and_content: sequencing depth normalized bigwig tracks
Library strategy: Cut-And-Run

source_name: U2OS cells

growth_protocol: Dox-inducible U2OS DDX41-GFP cells were cultured in DMEM medium containing 10% FBS, Pen-Strep, 1% Glutamine and 1µg/ml puromycine

extract_protocol:
Mnase activity was induced by addition of 3mM CaCl2 for 30 min on ice. Chromatin fragments were released by incubating the samples for 20 minutes at 37°C and centrifugation at 16.000×g for 10 minutes at 4°C. Supernatants were incubated at 70°C in the presence of 0.1% SDS and 5 µg proteinase K. DNA was cleaned-up using phenol/chloroform extraction
Libraries were prepared according to the Accel-NGS 1S Plus DNA Library Kit (Swift Bioscience) using the manufactures’ protocol suggested for the retention of small fragments ( 40 bp). Libraries were dual indexed and amplified by 14 cycles of PCR with Illumina primers, quantified and analyzed on a Tapestation device (Agilent), pooled in equimolar ratios and purified away from primer and adaptor dimers on a 2% agarose gel.

treatment_protocol: Cells were either treated with DMSO or 1 µg/ml docycycline for 48 h

value: U2OS cells (with dox-inducible expression of GFP-tagged DDX41 protein)

value: 1µg/ml doxycycline

value: Nanobody-GFP-Mnase

tag: replicate


title: U2OS cells, control_crosslink_rep2

value: DMSO


title: U2OS cells, control_crosslink_rep1


title: HCT116 cells, siCtrl_rep2

value: control


title: HCT116 cells, siDDX41_RnaseH1MNase_3

data_processing:
Library strategy: MapR
Base calling was performed with RTA v.2.4.11 and and demultiplexing was done using bcl2fastq v.2.19.1
Mapping was done against hg38 using bowtie2 (v. 2.3.4). Multi mapping reads were excluded from further analysis.
Sequencing depth normalised coverage tracks were created using Deeptools (v3.4.1)
Genome_build: hg38
Supplementary_files_format_and_content: sequencing depth normalised bigwig tracks

source_name: HCT116 cells, siDDX41_RnaseH1MNase

growth_protocol: HCT116 cells were cultured in RPMI1640 medium containing 10% FBS, Pen-Strep, 1% Glutamine

extract_protocol:
Mnase activity was induced by addition of 2mM CaCl2 for 30 min on ice. Chromatin fragments were released by incubating the samples for 20 minutes at 37°C and centrifugation at 16.000×g for 10 minutes at 4°C. Supernatants were incubated at 70°C in the presence of 0.1% SDS and 5 µg proteinase K. DNA was cleaned-up using phenol/chloroform extraction
NGS library preparation was performed using NuGEN´s Ovation Ultralow System V2 (M01379 v5). Libraries were prepared with a starting amount of 1 ng of DNA and were amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).

treatment_protocol: Knockdowns were induced for 48 hourse using pool siRNAs.

value: siDDX41 knockdown

value: RnaseH1MNase1 digestion


title: HCT116 cells, siDDX41_RnaseH1MNase_1


title: HCT116 cells, siDDX41_RnaseH1MNase_2


title: HCT116 cells, siCtrl_RnaseH1MNase_3

source_name: HCT116 cells, siCtrl_RnaseH1MNase

value: si control knockdown


title: HCT116 cells, siCtrl_rep1


title: Sample HT29-3D-3 technical replicate c

description: HT29 cell line 3D layer growth, sample 3 technical replicate c


title: Sample HT29-3D-1 technical replicate c

description: HT29 cell line 3D layer growth, sample 1 technical replicate c


title: HCT116 cells, siCtrl_RnaseH1MNase_2


title: Sample HT29-3D-1 technical replicate f

description: HT29 cell line 3D layer growth, sample 1 technical replicate f


title: HCT116 cells, siCtrl_pAMNase_3

source_name: HCT116 cells, siCtrl_pAMNase

value: pAMNase digestion


title: HCT116 cells, siCtrl_RnaseH1MNase_1


title: HCT116 cells, siDDX41_pAMNase_1

source_name: HCT116 cells, siDDX41_pAMNase


title: HCT116 cells, siCtrl_pAMNase_2


title: HCT116 cells, siCtrl_pAMNase_1


title: HCT116 cells, siDDX41_pAMNase_2


title: U2OS cells, DDX41_crosslink_rep2


title: C42-R3-DHT-NCOR2

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: processed data file: clusters.C42.NCOR2.DHT.pval.bed

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Alignment and peak calling from raw reads was performed using Rsubread/Csaw.
Genome_build: GRCh37
Supplementary_files_format_and_content: processed data is in supplementary files, consisting bed files from significantly enriched NCOR2 peaks identified over respective IgG controls.

source_name: PCa cell line

growth_protocol: Cells were maintained at 37oC and 5.0% CO2 using a cell culture incubator with UV contamination control. LNCaP and LNCaP-C4-2 cells were regularly maintained in RPMI 1640 Medium containing 10% FBS. All media was supplemented with 100 U/mL Penicillin-Streptomycin.

extract_protocol:
Total DNA was extracted from all samples using a standard phenol chloroform protocol
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility from 5ng total DNA

treatment_protocol: Cells were treated with indicated concentration of 10nM DHT or EtOH for 1 hr.

value: PCa cell line

tag: ip

tag: cell line source gender

value: male

value: 10nm DHT


title: C42-R3-DHT-IgG

value: IgG


title: C42-R3-EtOH-NCOR2

description: processed data file: clusters.C42.NCOR2.pval.bed

value: EtOH


title: C42-R2-DHT-IgG


title: C42-R2-DHT-NCOR2


title: C42-R2-EtOH-NCOR2


title: C42-R2-EtOH-IgG


title: C42-R1-DHT-NCOR2


title: C42-R1-EtOH-NCOR2


title: C42-R1-DHT-IgG


title: LNCaP-R3-DHT-NCOR2

description: processed data file: clusters.LNCaP.NCOR2.DHT.pval.bed

value: LNCaP


title: LNCaP-R3-EtOH-IgG

description: processed data file: clusters.LNCaP.NCOR2.pval.bed


title: LNCaP-R2-DHT-NCOR2


title: LNCaP-R3-DHT-IgG


title: LNCaP-R2-EtOH-NCOR2


title: C42-R1-EtOH-IgG


title: LNCaP-R2-DHT-IgG


title: C42-R3-EtOH-IgG


title: LNCaP-R1-EtOH-IgG


title: LNCaP-R2-EtOH-IgG


title: Mock_rep3

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
Basecalls performed using Real-Time Analysis (RTA) software v2.
Quality control of reads were performed using FASTQC.
Raw reads were aligned to a hg38 reference index based off of the human whole transcriptome assay which measures 19,283 genes (21,111 probes) using TempO-SeqR and the bowtie aligner, allowing for up to 2 mismatches in the 50-nucleotide target sequence.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts matrix of probes for the human whole transcriptome.

source_name: Primary HBVAF cells

growth_protocol: Quiescent primary HBVAFs (Sciencell, Carlsbad, CA) were co-cultured with either VZV-infected HBVAFs or uninfected HBVAFs (mock-infected) as described [PMID: 29159203].

extract_protocol:
Four thousand cells were lysed in 1X Lysis buffer (BioSpyder Technologies, Carlsbad, CA). Cell lysates were assayed using TempO-Seq whole human transcriptome targeted RNA sequencing plates , reagents, protocols, and software (BioSpyder Technologies).
Using a thermocycler, lysed samples were added to the TempO-Seq 96-well plates, coded adjacent primer pairs for each specific human transcript were annealed to sample RNA, primer pairs for each transcript ligated then amplified per manufacturer’s instructions .

treatment_protocol: HBVAFs were infected with VZV (200 plaque-forming units/cm2; VZV Gilden strain, GenBank No. MH379685) or with mock infection as described [PMID: 29159203]. Cells and supernatants (spun at 2000 RPM for 5 minutes to eliminate non-adherent VZV-infected cells [PMID: 29788447]) were analyzed at 3 days post-infection (DPI; height of cytopathic effect).

value: brain vascular adventitial fibroblasts

value: mock infection


title: LNCaP-R1-EtOH-NCOR2


title: LNCaP-R1-DHT-NCOR2


title: Mock_rep1


title: VZV_rep3

value: infected with VZV


title: LNCaP-R1-DHT-IgG


title: Mock_rep2


title: VZV_rep2


title: VZV_rep1


title: Gemci Carbo #2

city: LYON

first: Olivier

last: IMBAUD

state: Rhône-Alpes

address: Faculty of Medicine and Pharmacy - 3rd floor 8 Rockefeller Avenue

department: NeuroMyoGene Institut (INMG)

institute: UCBL | CNRS UMR 5310 | INSERM U1217

data_processing:
Demultiplexing was performed using Bcl2fastq v2.17.1.14
Trimming and quality check was performed using CutAdapt v1.9.1
Mapping was performed with STAR on Galaxy bioinformatic platform
Quantification was done  using HTSeq-count on Galaxy bioinformatic platform
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Avi-cell PDX MDAMB436

growth_protocol: Triple negative breast cancer cells (the MDA-MB-436 cell line) were implanted into series of chicken embryos

extract_protocol:
Extraction of total RNAs by column with DNAse step (Single Cell RNA  Purification kit, Norgen)  Quality control of total RNAs by profiles on Bioanalyzer 2100 (Agilent) and  quantification by Quantus fluorescence assay (Promega).
RNAseq libraries were prepared with 400 pg of total RNA with SMARTseq® Stranded Kit (Takara, Clontech)
Samples were sequenced in whole RNAseq using the NextSeq500 illumina Platform (75 bp single read).

treatment_protocol: Two treatments were injected intravenously: 1-excipient (= control = 0.9% NaCl); 2-a mix of gemcitabine and carboplatin.

value: mix of gemcitabine and carboplatin

value: Triple negative breast cancer cells (the MDA-MB-436 cell line) were transplanted into chicken embryos


title: control Nacl #2


title: HCT116 cells, siDDX41_pAMNase_3


title: control Nacl #1


title: Gemci Carbo #1


title: VAL - input DNA_rep1

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bwa-mem.
peaks were called using MACS
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using MACS
Supplementary_files_format_and_content: peak text files

source_name: VAL

extract_protocol:
Lysates were clarified from sonicated nuclei and FLI1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

value: VAL

value: lymphoma

tag: cell of origin

value: GCB

tag: chip antibody


title: VAL - input DNA_rep2

tag: cell line

tag: cell type


title: LNCaP-R3-EtOH-NCOR2


title: OCILy1 - input DNA_rep1


title: OCILy1 - input DNA_rep2


title: OCILy1 - FLI1_rep2

value: FLI1, Rabbit polyclonal anti-FLI1 (ab-15289, Abcam)


title: OCILy1 - FLI1_rep1


title: Male environmental enrichment (EE) cortical neurons - ATACseq - rep4

city: Cambridge

first: Ravikiran

last: Raju

state: MA

address: 15A Maple Ave

department: Picower Institute

institute: MIT

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9185

data_processing:
Illumina Casava1.7 software used for basecalling.
RNAseq processing from raw fastq: Star --runMode alignReads --outSAMtype BAM SortedByCoordinate --clip3pNbases 0 --clip5pNbases 3 (Star 2.5.4) --> DESeq2 dds[ rowSums(counts(dds)) > 1, ] (DESeq2 1.16.1) --> fdrtool statistic = "normal" method = "BH" (fdrtool 1.2.15)
ATACseq pocessing from raw fastq: samtools to remove duplicates and filter out mitochondrial reads (samtools 1.3.1) --> manual shifting of reads (bedtools bamtobed -bedpe -i ${out}.nsorted.rmdupNOS.noMt.bam 2>/dev/null | awk 'BEGIN {OFS="\t"}; {if($9 =="+") print $1,$2+4,$3+4,$4,$5-5,$6-5,$7,$8,$9,$10 ; else print $1,$2-5,$3-5,$4,$5+4,$6+4,$7,$8,$9,$10  }' > ${out}.shifted.rmdupNOS.noMt.bed) --> macs2 callpeak -f BAMPE -g mm -q 0.05 --nomodel --nolambda --keep-dup all (macs2 2.1.1) --> DiffBind for differenal peak analysis dba.analyze(contrastData, method=DBA_EDGER_CLASSIC) (DiffBind 3.2.2)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq processed files are counts per gene. ATAC-seq processed files are counts per peaks, with peak universe defined as peaks present in at least two samples. Of note for both experiments, males and females were processed and analyzed seprately.

source_name: NeuN(+) Cortical neurons

growth_protocol: Wildtype Swiss Webster mice were housed in normal condition until weaning at Postnatal Day 25

extract_protocol:
Animals were euthanized by exposure to isoflurane, and frontal cortices were dissected. Mortar and pestle were used to break up tissue in Phosphate Buffered Saline (ph 7.4, PBS) with cOmplete protease inhibitor cocktail (Roche) and RNaseOUT Recombinant Ribonuclease Inhibitor (ThermoFisher). Protease and ribonuclease inhibitors were present in all downstream steps. Tissue was then fixed using 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 20 minutes. Fixation was quenched with 1M Tris base (ph 8.0) to a final concentration of 250 mM of Tris. Tissue was washed twice in NF1 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 5 mM MgCl2, 0.1M sucrose, 0.5% Trixon X-100) to remove residual PFA and lyse cells for nuclear extraction. After washing, pellets were then resuspended in NF1 buffer for 30 rounds of dounce homogenization (Wheaton). After douncing, nuclear pellets were obtained by filtering sample through 70 micron mesh, and one more round of NF1 washing. Nuclear pellets were then resuspended in PBS with 1% Bovine Serum Albumin (BSA, ThermoFisher), and stained with Anti-NeuN antibody conjugated to Alexa Fluor 488 (clone A60, EMD Millipore) at a dilution of 1:2000 for 30 minutes. DAPI stain was also added at a concentration of 1:10,000 to aid in identification of nuclei when cell sorting.  After washing, nuclear suspension was subjected to fluorescence-activated cell sorting (FACS) on a BD FACS Aria II with 70 micron nozzle set to 70 PSI. Nuclei were identified via DAPI and neuronal nuclei were selected using the 488 channel. Sorted cells were immediately used for RNAseq or ATACseq library generation.
For RNAseq, Because tissues had been fixed prior to nuclear isolation, RNA was extracted from nuclei using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE Tissue (ThermoFisher). Nuclear RNA was run on an Agilent 2100 BioAnalyzer for quality control (sample statsitics provided in Supplementary Table 10). RNA libraries were generated using the SMARTer Stranded Total RNA-seq for mammalian samples (Takara). Of note, libraries were amplified using random hexamer primers so not enriched for mature transcripts. For ATACseq, ATACseq libraries were generated from sorted neuronal nuclei using the Nextera DNA Library Preparation Kit (Illumina), as described previously{Buenrostro:2013bc}. Briefly, nuclear pellet was resuspended in transposase reaction mix buffer, and transposase. Transposition reaction was performed for 30 minutes at 37 ℃. As described previously{Chen:2016kb}, ATACseq libraries can be generated from fixed nuclei. After transposase reaction, defixation buffer (50 mM Tris-HCl ph8.0, 1 mM EDTA, 0.2 M NaCl, 1% SDS, 5 ng/mL proteinase K) was added to the mixture, which was then incubated at 65 ℃ overnight with agitation at 1000 rpm on a benchtop shaker/heater block. The next morning, the reaction was purified using a Qiagen MinElute kit. Following purification, library fragments were amplified using Nextera PCR primers with cycling and cycling number determination as described in the original ATACseq paper cited above.

treatment_protocol: Mice were then placed in either Environmental Enrichment (EE) or Standard Housing (SH) conditions. Standard cages consisted of a 7 1⁄2” x 11 1⁄2” x 5” plastic chamber containing a layer of wood chip bedding and a single pulped cotton fiber nestlet. Enrichment cages were larger (10 1⁄2” x 19” x 8”) and contained a layer of wood chip bedding, 2-3 nestlets, Crink-l’Nest, a running wheel, a plastic tube, and three additional rodent toys replaced every 3-4 days. Food and water were provided ad libitum.

tag: Sex

value: Male

value: Environmental Enrichment

tag: age

value: 2 months


title: Male environmental enrichment (EE) cortical neurons - ATACseq - rep5

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9190


title: Male environmental enrichment (EE) cortical neurons - ATACseq - rep3

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9184


title: Male environmental enrichment (EE) cortical neurons - ATACseq - rep2

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9179


title: Male standard housed (SH) cortical neurons - ATACseq - rep7

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9194

value: Standard Housing


title: Male standard housed (SH) cortical neurons - ATACseq - rep6

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9193


title: Male environmental enrichment (EE) cortical neurons - ATACseq - rep1

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9178


title: Male standard housed (SH) cortical neurons - ATACseq - rep5

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9192


title: Male standard housed (SH) cortical neurons - ATACseq - rep4

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9187


title: Female environmental enrichment (EE) cortical neurons - ATACseq - rep3

description:
transposon-inserted genomic DNA
ATAC-seq signal
160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt
160718Tsa_D16-6843

value: Female


title: Male standard housed (SH) cortical neurons - ATACseq - rep2

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9181


title: VAL - FLI1_rep2


title: Male standard housed (SH) cortical neurons - ATACseq - rep1

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9180


title: Female environmental enrichment (EE) cortical neurons - ATACseq - rep2

description:
transposon-inserted genomic DNA
ATAC-seq signal
160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt
160718Tsa_D16-6842


title: VAL - FLI1_rep1


title: Female standard housed (SH) cortical neurons - ATACseq - rep2

description:
transposon-inserted genomic DNA
ATAC-seq signal
160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt
160718Tsa_D16-6841


title: Female environmental enrichment (EE) cortical neurons - ATACseq - rep1

description:
transposon-inserted genomic DNA
ATAC-seq signal
160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt
160718Tsa_D16-6839


title: Female standard housed (SH) cortical neurons - ATACseq - rep3

description:
transposon-inserted genomic DNA
ATAC-seq signal
160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt
160718Tsa_D16-6844


title: Female standard housed (SH) cortical neurons - ATACseq - rep1

description:
transposon-inserted genomic DNA
ATAC-seq signal
160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt
160718Tsa_D16-6838


title: Male environmental enrichment (EE) cortical neurons - ATACseq - rep6

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9191


title: Pogz_PFC _1

first: Zhen

last: Yan

address: 955 Main St

institute: SUNY Buffalo

data_processing:
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina) then sequencing was carried out with the HiSeq 2500 platform (Illumina)
Raw fastq paired-end sequencing reads were aligned to the mouse reference genome mm10 using RNA STAR
Gene expression of mapped reads were then measured using featureCounts, producing compatible gene expression matrices to be used for differential expression and downstream analysis.
We then used DEseq2 for differential gene expression analysis, with featureCounts data as input, under default settings.
Genome_build: mm10
Supplementary_files_format_and_content: bam file with genome alignment to mm10 genome

source_name: PFC

extract_protocol:
RNA extraction from PFC samples of biological duplicates in each group used the RNAeasy Mini kit (Qiagen), coupled to an RNase-free DNase step (Qiagen). The strand-specific RNA sequencing libraries were generated from 1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits (Illumina).
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina). Sequencing was carried out with the HiSeq 2500 platform (Illumina) at the Genomics and Bioinformatics Core of State University of New York at Buffalo.Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default parameters.

tag: tissue

value: Prefrontal Cortex (PFC)

value: Total cell lysate (bulk)

tag: strain

value: shRNA_ASH1L-AAV9 Injected


title: Pogz_PFC _2

tag: treatment


title: GFP_PFC_2 (Pogz Ctrl)

value: GFP-AAV9 Injected


title: Adnp_PFC_2


title: Adnp_PFC_1


title: GFP_PFC_1 (Pogz Ctrl)


title: GFP_PFC_2 (Adnp Ctrl)


title: GFP_PFC_1 (Adnp Ctrl)


title: Male standard housed (SH) cortical neurons - ATACseq - rep3

description:
transposon-inserted genomic DNA
ATAC-seq signal
171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt
171030TsaA_D17-9186


title: p1 astrocyte-ctrl_rep1

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragments Per Kilobase of transcript sequence per  Millions (FPKM) were calculated based on the length of the gene and reads count mapped  to this gene.FPKM considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample and genes.

source_name: p1 astrocyte

growth_protocol: Astrocytes were isolated from two P1 Tet1 WT or KO mice and cultured in a PDL-coated T25 flask for about 7 days. Astroctytes were purified with shaking at 260 rpm when reaching >95% plate coverage and cultured for another 24 hours before collection before RNA extraction.

extract_protocol:
total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cortex+hippocampus

value: astrocyte

value: untreated

tag: genotype

value: wild type

value: post natal day 1


title: p1 astrocyte-tet1ko_rep1


title: p1 astrocyte-tet1ko_rep2


title: Lum4

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

data_processing:
trimmomatic-0.35 was used for data trimming. Chop head 5bp of each read, slide the window with 4bp and trim the read with quality less than 20, the minimum length of read is 25bp and max length is 50bp
tophat-2.0.13 was used for alignment with default parameter for pair-end sequencin
cufflinks-2.2.1 was used with default parameter to get gene FPKM value
Genome_build: mm10
Supplementary_files_format_and_content: gene FPKM value for each sample were summarized in text file

source_name: Mouse mammary luminal cells

extract_protocol:
Mammary tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) according to the protocols of the manufacturer.

value: Mixed

value: Mammary

value: Brca1 knockout


title: Lum2


title: Lum1


title: Lum5


title: Lum3


title: SC9_96

description: total RNA

data_processing:
sickle was used for data quality control.
trim_galore-v0.4.1 was used for data trimming.
STAR-2.5.3a was used for alignment with default parameter for pair-end sequencing.
subread-1.5.3 was used for generation of read_count.
Genome_build: mm10
Supplementary_files_format_and_content: Gene read_count value for each sample were summarized in text file.

extract_protocol:
The sorted mammary luminal cells or tumor cells re-suspended in FACS buffer (300-500 cells/µL) were mixed (3:2 ratio) with C1 Cell Suspension Reagent (Fluidigm) before loading onto a  10 to 17-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm). Each capture site was carefully examined and recorded under a ZEISS microscope in bright field channel for cell doublets. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (protocol 100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (protocol 100-7168 E1).

treatment_protocol: Three-to-four month-old female virgin or pregnant at day 12.5 mice were sacrificed to isolate the fourth pair of mammary glands for single-cell preparation as previously described. In brief, the mammary glands were minced, washed in PBS and digested in DMEM/F12 containing 300 U/ml collagenase Ⅲ (S4M7602S, Worthington, Lakewood, NJ), 100 U/ml hyaluronidase (H3506; Sigma-Aldrich), 5% FBS (Gibco), 5 µg/ml insulin (350-020; Biosource, Rockville, MD), 10 ng/ml EGF (13247-051, Invitrogen), and 500 ng/ml hydrocortisone (H0888; Sigma-Aldrich) for about 1 hour at 37℃, 5% CO2. The resultant organoid suspension was sequentially re-suspended in DMEM/F12 supplemented with 5 mg/ml dispase II (825-001; Roche Diagnostics, Indianapolis, IN) and 0.1 mg/ml DNase I (58C10349; Worthington) for 5 min at 37℃, and then digested with 0.25% trypsin-EDTA for 1–2 min, and treated with RBC lysis buffer (00433-57; eBioscience, San Diego, CA) for 3 min to remove the red blood cells before filtration through a 40-µm cell strainer (352340, BD Falcon) to obtain single-cell suspension. Enrichment of Lin- epithelial cells was achieved through selective depletion of hematopoietic and endothelial cells by using the EasySeq mouse epithelial cell enrichment kit according to the manufacturer (19758; Stemcell). When the mammary tumors grew to around 1 cm in diameter, they were removed from the Brca1-defeicient mice for single-cell preparation as per the same method. The enriched Lin- mouse mammary epithelial cells and tumor cells were stained at a concentration of 1x106 cells per 100 μl of FACS buffer (HBSS with 0.5% BSA and 2 mM EDTA). Antibodies against mouse CD24 (anti CD24-PE-Cy™7, 560536, BD), and CD29 (anti CD29-APC, 102216, Biolegend) were used to stain the cells. DAPI (1 µg/ml) was also used as an indicator for cell viability. Antibody incubations were performed at 4℃ for 30 min. Then the cells were washed with PBS for twice before sorting by using FACSAria III Cell Sorter (Becton Dickinson). DAPI-CD24HiCD29LomGFP+ mammary luminal cells and CD24+ tumor cells were sorted out for following single cell RNA sequencing.

value: C57BL/6 and 129/Sv mixed

value: Mammary luminal

value: female


title: SC9_94

description: total RNA


title: SC9_91

description: total RNA


title: SC9_88

description: total RNA


title: SC9_85

description: total RNA


title: SC9_86

description: total RNA


title: SC9_90

description: total RNA


title: SC9_93

description: total RNA


title: SC9_87

description: total RNA


title: SC9_89

description: total RNA


title: SC9_84

description: total RNA


title: SC9_83

description: total RNA


title: SC9_76

description: total RNA


title: SC9_77

description: total RNA


title: SC9_82

description: total RNA


title: p1 astrocyte-ctrl_rep2


title: SC9_79

description: total RNA


title: SC9_75

description: total RNA