TRIM32 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-21	BGRSLV05-22
idx	0	0
TRCN#_or_BGC#	TRCN0000003455	TRCN0000003455
shRNA_or_gRNA_sequence	CCGGCAGGCAAGGTATAAAGCAGTTCTCGAGAACTGCTTTATACCTTGCCTGTTTTT	CCGGCAGGCAAGGTATAAAGCAGTTCTCGAGAACTGCTTTATACCTTGCCTGTTTTT
PAM
Name	TRIM32	TRIM32
Sample_ID	BGRSLV05-21	BGRSLV05-22
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	TRIM32	TRIM32
qPCR_result	57.1	57.9
Ave_qPCR	57.5
RT-qPCR_primer-F	ttaactcgtctgcgggaact
RT-qPCR_primer-R	gtccttggagacaccttcca
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	8474	8475

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-21	BGRSLV05-22
Sample_ID	BGRSLV05-21	BGRSLV05-22
Sample Name
Sample Name	TRIM32-BGRSLV05-21	TRIM32-BGRSLV05-22
RBP	TRIM32	TRIM32
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	11616	11617

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-21	BGRSLV05-22
Sample #	49	50
Sample Name	TRIM32-BGRSLV05-21	TRIM32-BGRSLV05-22
Sample_Name_Alias
Index Well Position	A07	B07
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	286	298
Peak_Molarity	47.40	75.50
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/E7.png	DNA_Library_set60-62/set1/F7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/A7.png	RNA_Library_set60-62/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-21	BGRSLV05-22
RBP	TRIM32	TRIM32
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	3636	3637

Sequencing Information

	BGRSLV05-21	BGRSLV05-22
Sample_ID	BGRSLV05-21	BGRSLV05-22
Sample Name	TRIM32-BGRSLV05-21	TRIM32-BGRSLV05-22
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	44,887,208	47,317,197
total_aligned_reads	30,816,349	23,554,188
unique_aligned_reads	28,677,600	21,834,205
percent_uniqueAligned	0.63888	0.46144
correlation_replicates	0.960804	0.960804
spikein_reads	94,784	66,340
percent_spikeins	0.00211	0.00140
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2507	2508

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
TRIM32-BGRSLV05-21_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2507	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	8606
TRIM32-BGRSLV05-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2507					GRCh38	V40	TRIM32-BGRSLV05-21_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM32-BGRSLV05-21_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10471
TRIM32-BGRSLV05-21_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	2507					GRCh38	V40	TRIM32-BGRSLV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	10523
TRIM32-BGRSLV05-21_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	2507					GRCh38	V40	TRIM32-BGRSLV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	10575
TRIM32-BGRSLV05-21_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	2507					GRCh38	V40	TRIM32-BGRSLV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	10627
TRIM32-BGRSLV05-21_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	2507					GRCh38	V40	TRIM32-BGRSLV05-21/Aligned.sortedByCoord.out.bam		ENCORE2	10679
TRIM32-BGRSLV05-21_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2507					GRCh38	V40	TRIM32-BGRSLV05-21_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM32-BGRSLV05-21_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10731
TRIM32-BGRSLV05-21_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2507	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	28873
TRIM32-BGRSLV05-22_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2508	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	8607
TRIM32-BGRSLV05-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2508					GRCh38	V40	TRIM32-BGRSLV05-22_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM32-BGRSLV05-22_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10472
TRIM32-BGRSLV05-22_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	2508					GRCh38	V40	TRIM32-BGRSLV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	10524
TRIM32-BGRSLV05-22_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	2508					GRCh38	V40	TRIM32-BGRSLV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	10576
TRIM32-BGRSLV05-22_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	2508					GRCh38	V40	TRIM32-BGRSLV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	10628
TRIM32-BGRSLV05-22_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	2508					GRCh38	V40	TRIM32-BGRSLV05-22/Aligned.sortedByCoord.out.bam		ENCORE2	10680
TRIM32-BGRSLV05-22_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2508					GRCh38	V40	TRIM32-BGRSLV05-22_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM32-BGRSLV05-22_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10732
TRIM32-BGRSLV05-22_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2508	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	28874