Nature - USA (2020-01-23)

4

nature research | reporting summary

April 2018

ChIP-seq

Data deposition

Confirm that both raw and final processed data have been deposited in a public database such as GEO.

Confirm that you have deposited or provided access to graph files (e.g. BED files) for the called peaks.

Data access links

May remain private before publication.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118765

The following secure token has been created to allow review of record GSE118765 while it remains in private status:

ersrqismjhypxex.

Files in database submission RAW FILES:

05_806_S4_Input_R1.combine.fastq.gz

06_806_S4_SB_SMAD23_R1.combine.fastq.gz

07_806_S4_TGFb_S23_R1.combine.fastq.gz

08_806_S4_RREB1_Input_R1.combine.fastq.gz

09_806_S4_RREB1_SB_HA_R1.combine.fastq.gz

10_806_S4_RREB1_TGFb_HA_R1.combine.fastq.gz

11_806_S4_RREB1_WT_Input_R1_001.fastq.gz

11_806_S4_RREB1_WT_Input_R2_001.fastq.gz

12_806_S4_RREB1_WT_SB_SMAD23_R1_001.fastq.gz

12_806_S4_RREB1_WT_SB_SMAD23_R2_001.fastq.gz

13_806_S4_RREB1_WT_TGFb_SMAD23_R1_001.fastq.gz

13_806_S4_RREB1_WT_TGFb_SMAD23_R2_001.fastq.gz

14_806_S4_RREB1_KO_Input_R1_001.fastq.gz

14_806_S4_RREB1_KO_Input_R2_001.fastq.gz

15_806_S4_RREB1_KO_SB_SMAD23_R1_001.fastq.gz

15_806_S4_RREB1_KO_SB_SMAD23_R2_001.fastq.gz

16_806_S4_RREB1_KO_TGFb_SMAD23_R1_001.fastq.gz

16_806_S4_RREB1_KO_TGFb_SMAD23_R2_001.fastq.gz

33_EB_D3_Input_R1_001.fastq.gz

33_EB_D3_Input_R2_001.fastq.gz

34_EB_D3_SMAD23_R1_001.fastq.gz

34_EB_D3_SMAD23_R2_001.fastq.gz

35_EB_D3_RREB1_R1_001.fastq.gz

35_EB_D3_RREB1_R2_001.fastq.gz

36_ATAC_EB_D3_R1_001.fastq.gz

36_ATAC_EB_D3_R2_001.fastq.gz

PROCESSED DATA FILES:

02_806_S4_Input_Tags.ucsc.bedGraph.gz

03_806_S4_SB_SMAD23_Tags.ucsc.bedGraph.gz

04_806_S4_TGFb_SMAD23_Tags.ucsc.bedGraph.gz

05_806_S4_RREB1_Input_Tags.ucsc.bedGraph.gz

06_806_S4_RREB1_SB_HA_Tags.ucsc.bedGraph.gz

07_806_S4_RREB1_TGFb_HA_Tags.ucsc.bedGraph.gz

08_806_S4_RREB1_WT_Input.sam_Tags.ucsc.bedGraph.gz

09_806_S4_RREB1_WT_SB_SMAD23.sam_Tags.ucsc.bedGraph.gz

10_806_S4_RREB1_WT_TGFb_SMAD23.sam_Tags.ucsc.bedGraph.gz

11_806_S4_RREB1_KO_Input.sam_Tags.ucsc.bedGraph.gz

12_806_S4_RREB1_KO_SB_SMAD23.sam_Tags.ucsc.bedGraph.gz

13_806_S4_RREB1_KO_TGFb_SMAD23.sam_Tags.ucsc.bedGraph.gz

16_EB_D3_Input_Tags.ucsc.bedGraph.gz

17_EB_D3_SMAD23_Tags.ucsc.bedGraph.gz

18_EB_D3_RREB1_Tags.ucsc.bedGraph.gz

19_ATAC_EB_D3_Tags.ucsc.bedGraph.gz

Genome browser session

(e.g. UCSC)

https://genome.ucsc.edu/cgi-bin/hgTracks?

hgS_doOtherUser=submit&hgS_otherUserName=suj&hgS_otherUserSessionName=Submission

Methodology

Replicates All ChIP-seq experiments were performed 1 or 2 times, and confirmed with ChIP-PCR experiment.

Sequencing depth 50 bp single-end or paired-end sequencing was performed to obtain 30 million read depth

Antibodies Rabbit monoclonal anti-SMAD2/3 Cell Signaling Technology Cat #8685; Rabbit monoclonal anti-HA-Tag Cell Signaling

Technology Cat #3724.

Peak calling parameters Peak calling from ChIP-Seq data was performed with MACS 1.4.2 and verified by HOMER (v4.10). The parameters for peak

calling included fold change >8, p value < 1e-8 to detect high confidence binding events. Input samples were used as

reference controls for background correction.