U2AF1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-17	BGRSLV02-18
idx	0	0
TRCN#_or_BGC#	TRCN0000001155	TRCN0000001155
shRNA_or_gRNA_sequence	GAAAGTGTTGTAGTTGATTGACTCGAGTCAATCAACTACAACACTTTC	GAAAGTGTTGTAGTTGATTGACTCGAGTCAATCAACTACAACACTTTC
PAM
Name	U2AF1	U2AF1
Sample_ID	BGRSLV02-17	BGRSLV02-18
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	U2AF1	U2AF1
qPCR_result	88.3	86.6
Ave_qPCR	87.4
RT-qPCR_primer-F	GTGACAACCTGGGAGACCAC
RT-qPCR_primer-R	GGTTATTCAAGTCAATCACAGCC
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	8254	8255

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-17	BGRSLV02-18
Sample_ID	BGRSLV02-17	BGRSLV02-18
Sample Name
Sample Name	U2AF1-BGRSLV02-17	U2AF1-BGRSLV02-18
RBP	U2AF1	U2AF1
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11304	11305

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-17	BGRSLV02-18
Sample #	7	8
Sample Name	U2AF1-BGRSLV02-17	U2AF1-BGRSLV02-18
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	285	279
Peak_Molarity	55.00	68.30
libSampleQC_DNA_Well	DNA_Library_set57/set1/G7.png	DNA_Library_set57/set1/H7.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set57/set1/G1.png	RNA_Library_set57/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-17	BGRSLV02-18
RBP	U2AF1	U2AF1
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3468	3469

Sequencing Information

	BGRSLV02-17	BGRSLV02-18
Sample_ID	BGRSLV02-17	BGRSLV02-18
Sample Name	U2AF1-BGRSLV02-17	U2AF1-BGRSLV02-18
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	48,058,258	33,648,351
total_aligned_reads	42,507,353	30,752,355
unique_aligned_reads	39,085,286	28,553,627
percent_uniqueAligned	0.81329	0.84859
correlation_replicates	0.955335	0.955335
spikein_reads	31,518	21,146
percent_spikeins	0.00066	0.00063
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2339	2340

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-BGRSLV02-17_S95_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2339	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8236
U2AF1-BGRSLV02-17_S95_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2339	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8282
U2AF1-BGRSLV02-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2339					GRCh38	V40	U2AF1-BGRSLV02-17_S95_L003_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSLV02-17_S95_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11525
U2AF1-BGRSLV02-17_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2339					GRCh38	V40	U2AF1-BGRSLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	11571
U2AF1-BGRSLV02-17_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2339					GRCh38	V40	U2AF1-BGRSLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	11617
U2AF1-BGRSLV02-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2339					GRCh38	V40	U2AF1-BGRSLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	11663
U2AF1-BGRSLV02-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2339					GRCh38	V40	U2AF1-BGRSLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	11709
U2AF1-BGRSLV02-17_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2339					GRCh38	V40	U2AF1-BGRSLV02-17_S95_L003_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSLV02-17_S95_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11755
U2AF1-BGRSLV02-18_S96_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2340	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8237
U2AF1-BGRSLV02-18_S96_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2340	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8283
U2AF1-BGRSLV02-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2340					GRCh38	V40	U2AF1-BGRSLV02-18_S96_L003_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSLV02-18_S96_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11526
U2AF1-BGRSLV02-18_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2340					GRCh38	V40	U2AF1-BGRSLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	11572
U2AF1-BGRSLV02-18_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2340					GRCh38	V40	U2AF1-BGRSLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	11618
U2AF1-BGRSLV02-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2340					GRCh38	V40	U2AF1-BGRSLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	11664
U2AF1-BGRSLV02-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2340					GRCh38	V40	U2AF1-BGRSLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	11710
U2AF1-BGRSLV02-18_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2340					GRCh38	V40	U2AF1-BGRSLV02-18_S96_L003_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSLV02-18_S96_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11756