TRNAU1AP RNA-Seq in 293T

Experiment Information (Status: NotSatisfied)

	BG293LV06-31	BG293LV06-32
idx	0	0
TRCN#_or_BGC#	TRCN0000160495	TRCN0000160495
shRNA_or_gRNA_sequence	CCGGCAACCAGTATTATCAGCAGTACTCGAGTACTGCTGATAATACTGGTTGTTTTTTG	CCGGCAACCAGTATTATCAGCAGTACTCGAGTACTGCTGATAATACTGGTTGTTTTTTG
PAM
Name	TRNAU1AP	TRNAU1AP
Sample_ID	BG293LV06-31	BG293LV06-32
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	TRNAU1AP	TRNAU1AP
qPCR_result	57.6	58.5
Ave_qPCR	58.1
RT-qPCR_primer-F
RT-qPCR_primer-R
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	12166	12167

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-31	BG293LV06-31	BG293LV06-32	BG293LV06-32
Sample_ID	BG293LV06-31	BG293LV06-31	BG293LV06-32	BG293LV06-32
Sample Name	TRNAU1AP-BG293LV06-31		TRNAU1AP-BG293LV06-32
Sample Name	TRNAU1AP-BG293LV06-31	TRNAU1AP-BG293LV06-31	TRNAU1AP-BG293LV06-32	TRNAU1AP-BG293LV06-32
RBP	TRNAU1AP	TRNAU1AP	TRNAU1AP	TRNAU1AP
Cell_Line	293T	293T	293T	293T
Exp UID
Status	NotSatisfied	Released	NotSatisfied	Released
Status_date	2024-10-16	2025-04-21	2024-10-16	2025-04-21
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13468	13570	13469	13571

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-31	BG293LV06-31	BG293LV06-32	BG293LV06-32
Sample #	35	133	36	134
Sample Name	TRNAU1AP-BG293LV06-31	TRNAU1AP-BG293LV06-31B	TRNAU1AP-BG293LV06-32	TRNAU1AP-BG293LV06-32B
Sample_Name_Alias
Index Well Position	C05	G01	D05	H01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-10-02	2024-09-25	2024-10-02
Lib_ID	Lib-240925B	Lib-241002	Lib-240925B	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	268	282	284	283
Peak_Molarity	4.52	70.00	107.00	81.90
libSampleQC_DNA_Well	DNA_Library_set71/set1/C5.png	DNA_Library_set72/set1/G1.png	DNA_Library_set71/set1/D5.png	DNA_Library_set72/set1/H1.png
RIN	10.0	9.9	10.0	9.9
libSample_RNA_Well	RNA_Library_set71/set1/C5.png	RNA_Library_set72/set1/G1.png	RNA_Library_set71/set1/D5.png	RNA_Library_set72/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-10-04	2024-09-30	2024-10-04
Sample_ID	BG293LV06-31	BG293LV06-31	BG293LV06-32	BG293LV06-32
RBP	TRNAU1AP	TRNAU1AP	TRNAU1AP	TRNAU1AP
Batch_ID	BG293LV06	BG293LV06	BG293LV06	BG293LV06
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	4460	4558	4461	4559

Sequencing Information

	BG293LV06-31	BG293LV06-31	BG293LV06-32	BG293LV06-32
Sample_ID	BG293LV06-31	BG293LV06-31	BG293LV06-32	BG293LV06-32
Sample Name	TRNAU1AP-BG293LV06-31	TRNAU1AP-BG293LV06-31B	TRNAU1AP-BG293LV06-32	TRNAU1AP-BG293LV06-32B
Pool ID	Pool-240930	Pool-241004	Pool-240930	Pool-241004
LocalServer_folder	set71	set72	set71	set72
total_reads	11,960,263	35,008,612	29,297,609	24,549,625
total_aligned_reads	8,810,291	32,072,795	26,500,291	21,720,575
unique_aligned_reads	8,207,231	29,971,634	24,854,402	20,311,281
percent_uniqueAligned	0.68621	0.85612	0.84834	0.82736
correlation_replicates	0.977186	0.998203	0.977186	0.998203
spikein_reads	26,274	132,650	70,044	103,720
percent_spikeins	0.00220	0.00379	0.00239	0.00422
original_ReadLength	101	101	101	101
QC_Status	LowNumReads	Submitted	OtherReasonsNotToSubmit	Submitted
ID	3029	3127	3030	3128

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
TRNAU1AP-BG293LV06-31B_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3127	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29824
TRNAU1AP-BG293LV06-31B_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3127	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29896
TRNAU1AP-BG293LV06-31B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3127					GRCh38	V40	TRNAU1AP-BG293LV06-31B_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BG293LV06-31B_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29968
TRNAU1AP-BG293LV06-31B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3127					GRCh38	V40	TRNAU1AP-BG293LV06-31B_Aligned.sortedByCoord.out.bam		ENCORE2	30040
TRNAU1AP-BG293LV06-31B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3127					GRCh38	V40	TRNAU1AP-BG293LV06-31B_Aligned.sortedByCoord.out.bam		ENCORE2	30112
TRNAU1AP-BG293LV06-31B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3127					GRCh38	V40	TRNAU1AP-BG293LV06-31B_Aligned.sortedByCoord.out.bam		ENCORE2	30184
TRNAU1AP-BG293LV06-31B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3127					GRCh38	V40	TRNAU1AP-BG293LV06-31B_Aligned.sortedByCoord.out.bam		ENCORE2	30256
TRNAU1AP-BG293LV06-31B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3127					GRCh38	V40	TRNAU1AP-BG293LV06-31B_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BG293LV06-31B_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30328
TRNAU1AP-BG293LV06-32B_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3128	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29825
TRNAU1AP-BG293LV06-32B_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3128	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29897
TRNAU1AP-BG293LV06-32B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3128					GRCh38	V40	TRNAU1AP-BG293LV06-32B_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BG293LV06-32B_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29969
TRNAU1AP-BG293LV06-32B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3128					GRCh38	V40	TRNAU1AP-BG293LV06-32B_Aligned.sortedByCoord.out.bam		ENCORE2	30041
TRNAU1AP-BG293LV06-32B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3128					GRCh38	V40	TRNAU1AP-BG293LV06-32B_Aligned.sortedByCoord.out.bam		ENCORE2	30113
TRNAU1AP-BG293LV06-32B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3128					GRCh38	V40	TRNAU1AP-BG293LV06-32B_Aligned.sortedByCoord.out.bam		ENCORE2	30185
TRNAU1AP-BG293LV06-32B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3128					GRCh38	V40	TRNAU1AP-BG293LV06-32B_Aligned.sortedByCoord.out.bam		ENCORE2	30257
TRNAU1AP-BG293LV06-32B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3128					GRCh38	V40	TRNAU1AP-BG293LV06-32B_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BG293LV06-32B_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30329