UBR7 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-61	BGRSLV04-62
idx	0	0
TRCN#_or_BGC#	TRCN0000037026	TRCN0000037026
shRNA_or_gRNA_sequence	CCGGCCTGCATGAAACGTTGTTCTTCTCGAGAAGAACAACGTTTCATGCAGGTTTTTG	CCGGCCTGCATGAAACGTTGTTCTTCTCGAGAAGAACAACGTTTCATGCAGGTTTTTG
PAM
Name	UBR7	UBR7
Sample_ID	BGRSLV04-61	BGRSLV04-62
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	UBR7	UBR7
qPCR_result	85.5	92.0
Ave_qPCR	88.8
RT-qPCR_primer-F	tccagaacagggaaaggatg
RT-qPCR_primer-R	gattctgcgttgaggctttc
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	8441	8442

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-61	BGRSLV04-62
Sample_ID	BGRSLV04-61	BGRSLV04-62
Sample Name
Sample Name	UBR7-BGRSLV04-61	UBR7-BGRSLV04-62
RBP	UBR7	UBR7
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	11468	11469

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-61	BGRSLV04-62
Sample #	33	34
Sample Name	UBR7-BGRSLV04-61	UBR7-BGRSLV04-62
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	284	292
Peak_Molarity	32.00	56.80
libSampleQC_DNA_Well	DNA_Library_set59/set1/A11.png	DNA_Library_set59/set1/B11.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set59/set1/A6.png	RNA_Library_set59/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-61	BGRSLV04-62
RBP	UBR7	UBR7
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3582	3583

Sequencing Information

	BGRSLV04-61	BGRSLV04-62
Sample_ID	BGRSLV04-61	BGRSLV04-62
Sample Name	UBR7-BGRSLV04-61	UBR7-BGRSLV04-62
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	70,652,435	58,934,615
total_aligned_reads	56,679,576	45,426,210
unique_aligned_reads	52,639,757	42,120,811
percent_uniqueAligned	0.74505	0.71470
correlation_replicates	0.991676	0.991676
spikein_reads	325,618	194,878
percent_spikeins	0.00461	0.00331
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2453	2454

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
UBR7-BGRSLV04-61_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2453	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8082
UBR7-BGRSLV04-61_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2453	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8120
UBR7-BGRSLV04-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2453					GRCh38	V40	UBR7-BGRSLV04-61_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBR7-BGRSLV04-61_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11051
UBR7-BGRSLV04-61_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2453					GRCh38	V40	UBR7-BGRSLV04-61/Aligned.sortedByCoord.out.bam		ENCORE2	11089
UBR7-BGRSLV04-61_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2453					GRCh38	V40	UBR7-BGRSLV04-61/Aligned.sortedByCoord.out.bam		ENCORE2	11127
UBR7-BGRSLV04-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2453					GRCh38	V40	UBR7-BGRSLV04-61/Aligned.sortedByCoord.out.bam		ENCORE2	11165
UBR7-BGRSLV04-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2453					GRCh38	V40	UBR7-BGRSLV04-61/Aligned.sortedByCoord.out.bam		ENCORE2	11203
UBR7-BGRSLV04-61_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2453					GRCh38	V40	UBR7-BGRSLV04-61_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBR7-BGRSLV04-61_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11241
UBR7-BGRSLV04-62_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2454	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8083
UBR7-BGRSLV04-62_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2454	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8121
UBR7-BGRSLV04-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2454					GRCh38	V40	UBR7-BGRSLV04-62_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBR7-BGRSLV04-62_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11052
UBR7-BGRSLV04-62_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2454					GRCh38	V40	UBR7-BGRSLV04-62/Aligned.sortedByCoord.out.bam		ENCORE2	11090
UBR7-BGRSLV04-62_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2454					GRCh38	V40	UBR7-BGRSLV04-62/Aligned.sortedByCoord.out.bam		ENCORE2	11128
UBR7-BGRSLV04-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2454					GRCh38	V40	UBR7-BGRSLV04-62/Aligned.sortedByCoord.out.bam		ENCORE2	11166
UBR7-BGRSLV04-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2454					GRCh38	V40	UBR7-BGRSLV04-62/Aligned.sortedByCoord.out.bam		ENCORE2	11204
UBR7-BGRSLV04-62_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2454					GRCh38	V40	UBR7-BGRSLV04-62_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBR7-BGRSLV04-62_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11242