CTCF RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-21	BGRSDLV02-22
idx	0	0
TRCN#_or_BGC#	TRCN0000230191	TRCN0000230191
shRNA_or_gRNA_sequence	CCGGCAAGAATGAGAAGCGCTTTAACTCGAGTTAAAGCGCTTCTCATTCTTGTTTTTG	CCGGCAAGAATGAGAAGCGCTTTAACTCGAGTTAAAGCGCTTCTCATTCTTGTTTTTG
PAM
Name	CTCF	CTCF
Sample_ID	BGRSDLV02-21	BGRSDLV02-22
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	CTCF	CTCF
qPCR_result	83.7	82.9
Ave_qPCR	83.3
RT-qPCR_primer-F	GGAAGAAAAAGAAAGATGCGCT
RT-qPCR_primer-R	TCAGGTTCAATTTCTACGGCA
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9232	9233

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-21	BGRSDLV02-22
Sample_ID	BGRSDLV02-21	BGRSDLV02-22
Sample Name
Sample Name	CTCF-BGRSDLV02-21	CTCF-BGRSDLV02-22
RBP	CTCF	CTCF
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12340	12341

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-21	BGRSDLV02-22
Sample #	21	22
Sample Name	CTCF-BGRSDLV02-21	CTCF-BGRSDLV02-22
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	281	287
Peak_Molarity	71.70	87.90
libSampleQC_DNA_Well	DNA_Library_set65/set1/E3.png	DNA_Library_set65/set1/F3.png
RIN	9.9	9.5
libSample_RNA_Well	RNA_Library_set65/set1/E3.png	RNA_Library_set65/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-21	BGRSDLV02-22
RBP	CTCF	CTCF
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3942	3943

Sequencing Information

	BGRSDLV02-21	BGRSDLV02-22
Sample_ID	BGRSDLV02-21	BGRSDLV02-22
Sample Name	CTCF-BGRSDLV02-21	CTCF-BGRSDLV02-22
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	45,836,855	29,042,468
total_aligned_reads	38,677,778	26,036,125
unique_aligned_reads	35,715,343	24,133,747
percent_uniqueAligned	0.77918	0.83098
correlation_replicates	0.991263	0.991263
spikein_reads	850	7,884
percent_spikeins	0.00002	0.00027
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2689	2690

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
CTCF-BGRSDLV02-21_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2689	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8758
CTCF-BGRSDLV02-21_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2689	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8834
CTCF-BGRSDLV02-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2689					GRCh38	V40	CTCF-BGRSDLV02-21_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-21_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9323
CTCF-BGRSDLV02-21_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2689					GRCh38	V40	CTCF-BGRSDLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	9399
CTCF-BGRSDLV02-21_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2689					GRCh38	V40	CTCF-BGRSDLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	9475
CTCF-BGRSDLV02-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2689					GRCh38	V40	CTCF-BGRSDLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	9551
CTCF-BGRSDLV02-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2689					GRCh38	V40	CTCF-BGRSDLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	9627
CTCF-BGRSDLV02-21_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2689					GRCh38	V40	CTCF-BGRSDLV02-21_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-21_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9703
CTCF-BGRSDLV02-22_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2690	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8759
CTCF-BGRSDLV02-22_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2690	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8835
CTCF-BGRSDLV02-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2690					GRCh38	V40	CTCF-BGRSDLV02-22_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-22_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9324
CTCF-BGRSDLV02-22_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2690					GRCh38	V40	CTCF-BGRSDLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	9400
CTCF-BGRSDLV02-22_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2690					GRCh38	V40	CTCF-BGRSDLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	9476
CTCF-BGRSDLV02-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2690					GRCh38	V40	CTCF-BGRSDLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	9552
CTCF-BGRSDLV02-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2690					GRCh38	V40	CTCF-BGRSDLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	9628
CTCF-BGRSDLV02-22_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2690					GRCh38	V40	CTCF-BGRSDLV02-22_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGRSDLV02-22_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9704