USP39 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-39	BGRSLV05-40
idx	0	0
TRCN#_or_BGC#	TRCN0000001151	TRCN0000001151
shRNA_or_gRNA_sequence	CCGGCCTTCCAGACAACTATGAGATCTCGAGATCTCATAGTTGTCTGGAAGGTTTTT	CCGGCCTTCCAGACAACTATGAGATCTCGAGATCTCATAGTTGTCTGGAAGGTTTTT
PAM
Name	USP39	USP39
Sample_ID	BGRSLV05-39	BGRSLV05-40
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	USP39	USP39
qPCR_result	94.7	93.5
Ave_qPCR	94.1
RT-qPCR_primer-F	caacctccacaccctcaagt
RT-qPCR_primer-R	gcaatttgctgctttgtgaa
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	8492	8493

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-39	BGRSLV05-40
Sample_ID	BGRSLV05-39	BGRSLV05-40
Sample Name
Sample Name	USP39-BGRSLV05-39	USP39-BGRSLV05-40
RBP	USP39	USP39
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	11622	11623

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-39	BGRSLV05-40
Sample #	55	56
Sample Name	USP39-BGRSLV05-39	USP39-BGRSLV05-40
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	298	290
Peak_Molarity	88.80	127.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/C8.png	DNA_Library_set60-62/set1/D8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/G7.png	RNA_Library_set60-62/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-39	BGRSLV05-40
RBP	USP39	USP39
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3642	3643

Sequencing Information

	BGRSLV05-39	BGRSLV05-40
Sample_ID	BGRSLV05-39	BGRSLV05-40
Sample Name	USP39-BGRSLV05-39	USP39-BGRSLV05-40
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	29,583,115	36,122,933
total_aligned_reads	25,832,945	30,307,144
unique_aligned_reads	24,048,067	28,249,654
percent_uniqueAligned	0.81290	0.78204
correlation_replicates	0.998863	0.998863
spikein_reads	3,178	71,230
percent_spikeins	0.00011	0.00197
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2513	2514

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
USP39-BGRSLV05-39_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2513	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8614
USP39-BGRSLV05-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2513					GRCh38	V40	USP39-BGRSLV05-39_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGRSLV05-39_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10479
USP39-BGRSLV05-39_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2513					GRCh38	V40	USP39-BGRSLV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	10531
USP39-BGRSLV05-39_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2513					GRCh38	V40	USP39-BGRSLV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	10583
USP39-BGRSLV05-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2513					GRCh38	V40	USP39-BGRSLV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	10635
USP39-BGRSLV05-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2513					GRCh38	V40	USP39-BGRSLV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	10687
USP39-BGRSLV05-39_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2513					GRCh38	V40	USP39-BGRSLV05-39_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGRSLV05-39_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10739
USP39-BGRSLV05-39_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2513	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28881
USP39-BGRSLV05-40_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2514	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8615
USP39-BGRSLV05-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2514					GRCh38	V40	USP39-BGRSLV05-40_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGRSLV05-40_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10480
USP39-BGRSLV05-40_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2514					GRCh38	V40	USP39-BGRSLV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	10532
USP39-BGRSLV05-40_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2514					GRCh38	V40	USP39-BGRSLV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	10584
USP39-BGRSLV05-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2514					GRCh38	V40	USP39-BGRSLV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	10636
USP39-BGRSLV05-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2514					GRCh38	V40	USP39-BGRSLV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	10688
USP39-BGRSLV05-40_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2514					GRCh38	V40	USP39-BGRSLV05-40_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGRSLV05-40_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10740
USP39-BGRSLV05-40_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2514	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28882