APEX2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-7dox	BGRSDLV02-8dox
idx	0	0
TRCN#_or_BGC#	TRCN0000049659	TRCN0000049659
shRNA_or_gRNA_sequence	CCGGGCTTCTATCGTTTGCTGCAAACTCGAGTTTGCAGCAAACGATAGAAGCTTTTTG	CCGGGCTTCTATCGTTTGCTGCAAACTCGAGTTTGCAGCAAACGATAGAAGCTTTTTG
PAM
Name	APEX2	APEX2
Sample_ID	BGRSDLV02-7dox	BGRSDLV02-8dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	APEX2	APEX2
qPCR_result	75.0	67.8
Ave_qPCR	71.4
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9218	9219

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-7dox	BGRSDLV02-8dox
Sample_ID	BGRSDLV02-7dox	BGRSDLV02-8dox
Sample Name
Sample Name	APEX2-BGRSDLV02-7dox	APEX2-BGRSDLV02-8dox
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	12326	12327

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-7dox	BGRSDLV02-8dox
Sample #	7	8
Sample Name	APEX2-BGRSDLV02-7dox	APEX2-BGRSDLV02-8dox
Sample_Name_Alias
Index Well Position	G01	H01
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	296	289
Peak_Molarity	56.10	45.00
libSampleQC_DNA_Well	DNA_Library_set65/set1/G1.png	DNA_Library_set65/set1/H1.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set65/set1/G1.png	RNA_Library_set65/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-7dox	BGRSDLV02-8dox
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	3928	3929

Sequencing Information

	BGRSDLV02-7dox	BGRSDLV02-8dox
Sample_ID	BGRSDLV02-7dox	BGRSDLV02-8dox
Sample Name	APEX2-BGRSDLV02-7dox	APEX2-BGRSDLV02-8dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	28,184,081	31,740,668
total_aligned_reads	24,793,105	27,227,229
unique_aligned_reads	23,248,488	25,545,233
percent_uniqueAligned	0.82488	0.80481
correlation_replicates	0.998198	0.998198
spikein_reads	6,036	8,760
percent_spikeins	0.00021	0.00028
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2675	2676

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-BGRSDLV02-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2675	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8740
APEX2-BGRSDLV02-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2675	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8816
APEX2-BGRSDLV02-7dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2675					GRCh38	V40	APEX2-BGRSDLV02-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9305
APEX2-BGRSDLV02-7dox_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	2675					GRCh38	V40	APEX2-BGRSDLV02-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9381
APEX2-BGRSDLV02-7dox_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	2675					GRCh38	V40	APEX2-BGRSDLV02-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9457
APEX2-BGRSDLV02-7dox_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	2675					GRCh38	V40	APEX2-BGRSDLV02-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9533
APEX2-BGRSDLV02-7dox_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	2675					GRCh38	V40	APEX2-BGRSDLV02-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	9609
APEX2-BGRSDLV02-7dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2675					GRCh38	V40	APEX2-BGRSDLV02-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9685
APEX2-BGRSDLV02-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2676	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8741
APEX2-BGRSDLV02-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2676	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8817
APEX2-BGRSDLV02-8dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2676					GRCh38	V40	APEX2-BGRSDLV02-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9306
APEX2-BGRSDLV02-8dox_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	2676					GRCh38	V40	APEX2-BGRSDLV02-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9382
APEX2-BGRSDLV02-8dox_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	2676					GRCh38	V40	APEX2-BGRSDLV02-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9458
APEX2-BGRSDLV02-8dox_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	2676					GRCh38	V40	APEX2-BGRSDLV02-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9534
APEX2-BGRSDLV02-8dox_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	2676					GRCh38	V40	APEX2-BGRSDLV02-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	9610
APEX2-BGRSDLV02-8dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2676					GRCh38	V40	APEX2-BGRSDLV02-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,APEX2-BGRSDLV02-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9686