U2AF1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-7dox	BGRSDLV04-8dox
idx	0	0
TRCN#_or_BGC#	TRCN0000001155	TRCN0000001155
shRNA_or_gRNA_sequence	GAAAGTGTTGTAGTTGATTGACTCGAGTCAATCAACTACAACACTTTC	GAAAGTGTTGTAGTTGATTGACTCGAGTCAATCAACTACAACACTTTC
PAM
Name	U2AF1	U2AF1
Sample_ID	BGRSDLV04-7dox	BGRSDLV04-8dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	U2AF1	U2AF1
qPCR_result	90.59546	90.41007
Ave_qPCR	90.502765
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	9371	9372

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-7dox	BGRSDLV04-8dox
Sample_ID	BGRSDLV04-7dox	BGRSDLV04-8dox
Sample Name
Sample Name	U2AF1-BGRSDLV04-7dox	U2AF1-BGRSDLV04-8dox
RBP	U2AF1	U2AF1
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12652	12653

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-7dox	BGRSDLV04-8dox
Sample #	7	8
Sample Name	U2AF1-BGRSDLV04-7dox	U2AF1-BGRSDLV04-8dox
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	286	288
Peak_Molarity	25.80	28.80
libSampleQC_DNA_Well	DNA_Library_set68/set1/G1.png	DNA_Library_set68/set1/H1.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set68/set1/G1.png	RNA_Library_set68/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-7dox	BGRSDLV04-8dox
RBP	U2AF1	U2AF1
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4080	4081

Sequencing Information

	BGRSDLV04-7dox	BGRSDLV04-8dox
Sample_ID	BGRSDLV04-7dox	BGRSDLV04-8dox
Sample Name	U2AF1-BGRSDLV04-7dox	U2AF1-BGRSDLV04-8dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	29,694,156	26,249,010
total_aligned_reads	22,943,184	20,663,351
unique_aligned_reads	21,440,887	19,349,192
percent_uniqueAligned	0.72206	0.73714
correlation_replicates	0.999602	0.999602
spikein_reads	4,444	8,490
percent_spikeins	0.00015	0.00032
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2843	2844

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
U2AF1-BGRSDLV04-7dox_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2843	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27671
U2AF1-BGRSDLV04-7dox_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2843	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27735
U2AF1-BGRSDLV04-7dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2843					GRCh38	V40	U2AF1-BGRSDLV04-7dox_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-7dox_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27799
U2AF1-BGRSDLV04-7dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2843					GRCh38	V40	U2AF1-BGRSDLV04-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	27863
U2AF1-BGRSDLV04-7dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2843					GRCh38	V40	U2AF1-BGRSDLV04-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	27927
U2AF1-BGRSDLV04-7dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2843					GRCh38	V40	U2AF1-BGRSDLV04-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	27991
U2AF1-BGRSDLV04-7dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2843					GRCh38	V40	U2AF1-BGRSDLV04-7dox/Aligned.sortedByCoord.out.bam		ENCORE2	28055
U2AF1-BGRSDLV04-7dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2843					GRCh38	V40	U2AF1-BGRSDLV04-7dox_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-7dox_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28119
U2AF1-BGRSDLV04-8dox_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2844	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27672
U2AF1-BGRSDLV04-8dox_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2844	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27736
U2AF1-BGRSDLV04-8dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2844					GRCh38	V40	U2AF1-BGRSDLV04-8dox_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-8dox_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27800
U2AF1-BGRSDLV04-8dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2844					GRCh38	V40	U2AF1-BGRSDLV04-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	27864
U2AF1-BGRSDLV04-8dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2844					GRCh38	V40	U2AF1-BGRSDLV04-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	27928
U2AF1-BGRSDLV04-8dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2844					GRCh38	V40	U2AF1-BGRSDLV04-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	27992
U2AF1-BGRSDLV04-8dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2844					GRCh38	V40	U2AF1-BGRSDLV04-8dox/Aligned.sortedByCoord.out.bam		ENCORE2	28056
U2AF1-BGRSDLV04-8dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2844					GRCh38	V40	U2AF1-BGRSDLV04-8dox_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-8dox_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28120