TRMU RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-27	BGRSLV05-28
idx	0	0
TRCN#_or_BGC#	TRCN0000034600	TRCN0000034600
shRNA_or_gRNA_sequence	CCGGCCTGGTCACTTTATTTCCATACTCGAGTATGGAAATAAAGTGACCAGGTTTTTG	CCGGCCTGGTCACTTTATTTCCATACTCGAGTATGGAAATAAAGTGACCAGGTTTTTG
PAM
Name	TRMU	TRMU
Sample_ID	BGRSLV05-27	BGRSLV05-28
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	TRMU	TRMU
qPCR_result	58.9	58.7
Ave_qPCR	58.8
RT-qPCR_primer-F	gggccagagagcaaacatag
RT-qPCR_primer-R	gtcctcagcaggtccctgta
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	8480	8481

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-27	BGRSLV05-28
Sample_ID	BGRSLV05-27	BGRSLV05-28
Sample Name
Sample Name	TRMU-BGRSLV05-27	TRMU-BGRSLV05-28
RBP	TRMU	TRMU
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	11618	11619

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-27	BGRSLV05-28
Sample #	51	52
Sample Name	TRMU-BGRSLV05-27	TRMU-BGRSLV05-28
Sample_Name_Alias
Index Well Position	C07	D07
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	289	302
Peak_Molarity	91.00	73.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G7.png	DNA_Library_set60-62/set1/H7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/C7.png	RNA_Library_set60-62/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-27	BGRSLV05-28
RBP	TRMU	TRMU
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	3638	3639

Sequencing Information

	BGRSLV05-27	BGRSLV05-28
Sample_ID	BGRSLV05-27	BGRSLV05-28
Sample Name	TRMU-BGRSLV05-27	TRMU-BGRSLV05-28
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	28,937,313	25,289,193
total_aligned_reads	23,826,476	22,744,061
unique_aligned_reads	22,189,020	21,264,395
percent_uniqueAligned	0.76680	0.84085
correlation_replicates	0.992405	0.992405
spikein_reads	53,184	41,792
percent_spikeins	0.00184	0.00165
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2509	2510

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
TRMU-BGRSLV05-27_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2509	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	8608
TRMU-BGRSLV05-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2509					GRCh38	V40	TRMU-BGRSLV05-27_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRMU-BGRSLV05-27_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10473
TRMU-BGRSLV05-27_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	2509					GRCh38	V40	TRMU-BGRSLV05-27/Aligned.sortedByCoord.out.bam		ENCORE2	10525
TRMU-BGRSLV05-27_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	2509					GRCh38	V40	TRMU-BGRSLV05-27/Aligned.sortedByCoord.out.bam		ENCORE2	10577
TRMU-BGRSLV05-27_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	2509					GRCh38	V40	TRMU-BGRSLV05-27/Aligned.sortedByCoord.out.bam		ENCORE2	10629
TRMU-BGRSLV05-27_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	2509					GRCh38	V40	TRMU-BGRSLV05-27/Aligned.sortedByCoord.out.bam		ENCORE2	10681
TRMU-BGRSLV05-27_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2509					GRCh38	V40	TRMU-BGRSLV05-27_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRMU-BGRSLV05-27_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10733
TRMU-BGRSLV05-27_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2509	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	28875
TRMU-BGRSLV05-28_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2510	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	8609
TRMU-BGRSLV05-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2510					GRCh38	V40	TRMU-BGRSLV05-28_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRMU-BGRSLV05-28_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10474
TRMU-BGRSLV05-28_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	2510					GRCh38	V40	TRMU-BGRSLV05-28/Aligned.sortedByCoord.out.bam		ENCORE2	10526
TRMU-BGRSLV05-28_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	2510					GRCh38	V40	TRMU-BGRSLV05-28/Aligned.sortedByCoord.out.bam		ENCORE2	10578
TRMU-BGRSLV05-28_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	2510					GRCh38	V40	TRMU-BGRSLV05-28/Aligned.sortedByCoord.out.bam		ENCORE2	10630
TRMU-BGRSLV05-28_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	2510					GRCh38	V40	TRMU-BGRSLV05-28/Aligned.sortedByCoord.out.bam		ENCORE2	10682
TRMU-BGRSLV05-28_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2510					GRCh38	V40	TRMU-BGRSLV05-28_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRMU-BGRSLV05-28_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10734
TRMU-BGRSLV05-28_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2510	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	28876