USP44 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-63	BGRSLV04-64
idx	0	0
TRCN#_or_BGC#	TRCN0000038814	TRCN0000038814
shRNA_or_gRNA_sequence	CCGGCGGATGATGAACTTGTGCAATCTCGAGATTGCACAAGTTCATCATCCGTTTTTG	CCGGCGGATGATGAACTTGTGCAATCTCGAGATTGCACAAGTTCATCATCCGTTTTTG
PAM
Name	USP44	USP44
Sample_ID	BGRSLV04-63	BGRSLV04-64
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	USP44	USP44
qPCR_result	85.1	67.0
Ave_qPCR	76.0
RT-qPCR_primer-F	CTACCTCAGGTTCTCAGACTGC
RT-qPCR_primer-R	TCTGAGGGATTTCAGGGTCTCC
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	8443	8444

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-63	BGRSLV04-64
Sample_ID	BGRSLV04-63	BGRSLV04-64
Sample Name
Sample Name	USP44-BGRSLV04-63	USP44-BGRSLV04-64
RBP	USP44	USP44
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	11470	11471

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-63	BGRSLV04-64
Sample #	35	36
Sample Name	USP44-BGRSLV04-63	USP44-BGRSLV04-64
Sample_Name_Alias
Index Well Position	C05	D05
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	295	283
Peak_Molarity	74.50	62.80
libSampleQC_DNA_Well	DNA_Library_set59/set1/C11.png	DNA_Library_set59/set1/D11.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set59/set1/C6.png	RNA_Library_set59/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-63	BGRSLV04-64
RBP	USP44	USP44
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	3584	3585

Sequencing Information

	BGRSLV04-63	BGRSLV04-64
Sample_ID	BGRSLV04-63	BGRSLV04-64
Sample Name	USP44-BGRSLV04-63	USP44-BGRSLV04-64
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	80,768,650	51,207,700
total_aligned_reads	71,687,539	39,879,318
unique_aligned_reads	66,618,504	37,021,018
percent_uniqueAligned	0.82481	0.72296
correlation_replicates	0.990000	0.990000
spikein_reads	252,434	127,720
percent_spikeins	0.00313	0.00249
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2455	2456

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
USP44-BGRSLV04-63_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2455	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	8084
USP44-BGRSLV04-63_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2455	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	8122
USP44-BGRSLV04-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2455					GRCh38	V40	USP44-BGRSLV04-63_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP44-BGRSLV04-63_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11053
USP44-BGRSLV04-63_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	2455					GRCh38	V40	USP44-BGRSLV04-63/Aligned.sortedByCoord.out.bam		ENCORE2	11091
USP44-BGRSLV04-63_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	2455					GRCh38	V40	USP44-BGRSLV04-63/Aligned.sortedByCoord.out.bam		ENCORE2	11129
USP44-BGRSLV04-63_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	2455					GRCh38	V40	USP44-BGRSLV04-63/Aligned.sortedByCoord.out.bam		ENCORE2	11167
USP44-BGRSLV04-63_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	2455					GRCh38	V40	USP44-BGRSLV04-63/Aligned.sortedByCoord.out.bam		ENCORE2	11205
USP44-BGRSLV04-63_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2455					GRCh38	V40	USP44-BGRSLV04-63_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP44-BGRSLV04-63_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11243
USP44-BGRSLV04-64_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2456	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	8085
USP44-BGRSLV04-64_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2456	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	8123
USP44-BGRSLV04-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2456					GRCh38	V40	USP44-BGRSLV04-64_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP44-BGRSLV04-64_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11054
USP44-BGRSLV04-64_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	2456					GRCh38	V40	USP44-BGRSLV04-64/Aligned.sortedByCoord.out.bam		ENCORE2	11092
USP44-BGRSLV04-64_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	2456					GRCh38	V40	USP44-BGRSLV04-64/Aligned.sortedByCoord.out.bam		ENCORE2	11130
USP44-BGRSLV04-64_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	2456					GRCh38	V40	USP44-BGRSLV04-64/Aligned.sortedByCoord.out.bam		ENCORE2	11168
USP44-BGRSLV04-64_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	2456					GRCh38	V40	USP44-BGRSLV04-64/Aligned.sortedByCoord.out.bam		ENCORE2	11206
USP44-BGRSLV04-64_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2456					GRCh38	V40	USP44-BGRSLV04-64_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP44-BGRSLV04-64_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11244