APEX2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-5	BGRSDLV02-6
idx	0	0
TRCN#_or_BGC#	TRCN0000049659	TRCN0000049659
shRNA_or_gRNA_sequence	CCGGGCTTCTATCGTTTGCTGCAAACTCGAGTTTGCAGCAAACGATAGAAGCTTTTTG	CCGGGCTTCTATCGTTTGCTGCAAACTCGAGTTTGCAGCAAACGATAGAAGCTTTTTG
PAM
Name	APEX2	APEX2
Sample_ID	BGRSDLV02-5	BGRSDLV02-6
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	APEX2	APEX2
qPCR_result	69.1	73.7
Ave_qPCR	71.4
RT-qPCR_primer-F	gcctgagcggctagtcttta
RT-qPCR_primer-R	ggtcacccagaatgatcaca
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	9216	9217

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-5	BGRSDLV02-6
Sample_ID	BGRSDLV02-5	BGRSDLV02-6
Sample Name
Sample Name	APEX2-BGRSDLV02-5	APEX2-BGRSDLV02-6
RBP	APEX2	APEX2
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12324	12325

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-5	BGRSDLV02-6
Sample #	5	6
Sample Name	APEX2-BGRSDLV02-5	APEX2-BGRSDLV02-6
Sample_Name_Alias
Index Well Position	E01	F01
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	302	292
Peak_Molarity	57.70	69.60
libSampleQC_DNA_Well	DNA_Library_set65/set1/E1.png	DNA_Library_set65/set1/F1.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set65/set1/E1.png	RNA_Library_set65/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-5	BGRSDLV02-6
RBP	APEX2	APEX2
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	3926	3927

Sequencing Information

	BGRSDLV02-5	BGRSDLV02-6
Sample_ID	BGRSDLV02-5	BGRSDLV02-6
Sample Name	APEX2-BGRSDLV02-5	APEX2-BGRSDLV02-6
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	31,472,759	21,887,483
total_aligned_reads	26,412,154	19,119,953
unique_aligned_reads	24,754,624	17,950,278
percent_uniqueAligned	0.78654	0.82012
correlation_replicates	0.997493	0.997493
spikein_reads	5,730	6,142
percent_spikeins	0.00018	0.00028
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2673	2674

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
APEX2-BGRSDLV02-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2673	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	8738
APEX2-BGRSDLV02-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2673	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	8814
APEX2-BGRSDLV02-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2673					GRCh38	V40	APEX2-BGRSDLV02-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9303
APEX2-BGRSDLV02-5_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	2673					GRCh38	V40	APEX2-BGRSDLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	9379
APEX2-BGRSDLV02-5_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	2673					GRCh38	V40	APEX2-BGRSDLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	9455
APEX2-BGRSDLV02-5_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	2673					GRCh38	V40	APEX2-BGRSDLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	9531
APEX2-BGRSDLV02-5_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	2673					GRCh38	V40	APEX2-BGRSDLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	9607
APEX2-BGRSDLV02-5_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2673					GRCh38	V40	APEX2-BGRSDLV02-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9683
APEX2-BGRSDLV02-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2674	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	8739
APEX2-BGRSDLV02-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2674	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	8815
APEX2-BGRSDLV02-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2674					GRCh38	V40	APEX2-BGRSDLV02-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9304
APEX2-BGRSDLV02-6_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	2674					GRCh38	V40	APEX2-BGRSDLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	9380
APEX2-BGRSDLV02-6_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	2674					GRCh38	V40	APEX2-BGRSDLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	9456
APEX2-BGRSDLV02-6_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	2674					GRCh38	V40	APEX2-BGRSDLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	9532
APEX2-BGRSDLV02-6_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	2674					GRCh38	V40	APEX2-BGRSDLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	9608
APEX2-BGRSDLV02-6_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2674					GRCh38	V40	APEX2-BGRSDLV02-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9684