NDUFS6 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-23	BGRSLV04-24
idx	0	0
TRCN#_or_BGC#	TRCN0000036649	TRCN0000036649
shRNA_or_gRNA_sequence	CCGGCGTCAGAAAGAGGTGAATGAACTCGAGTTCATTCACCTCTTTCTGACGTTTTTG	CCGGCGTCAGAAAGAGGTGAATGAACTCGAGTTCATTCACCTCTTTCTGACGTTTTTG
PAM
Name	NDUFS6	NDUFS6
Sample_ID	BGRSLV04-23	BGRSLV04-24
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	NDUFS6	NDUFS6
qPCR_result	97.6	98.0
Ave_qPCR	97.8
RT-qPCR_primer-F	aagactacaggagaattcggtttg
RT-qPCR_primer-R	tacacttttgggtggccaag
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	8403	8404

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-23	BGRSLV04-24
Sample_ID	BGRSLV04-23	BGRSLV04-24
Sample Name
Sample Name	NDUFS6-BGRSLV04-23	NDUFS6-BGRSLV04-24
RBP	NDUFS6	NDUFS6
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	11446	11447

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-23	BGRSLV04-24
Sample #	11	12
Sample Name	NDUFS6-BGRSLV04-23	NDUFS6-BGRSLV04-24
Sample_Name_Alias
Index Well Position	C02	D02
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	294	290
Peak_Molarity	55.90	69.90
libSampleQC_DNA_Well	DNA_Library_set59/set1/C8.png	DNA_Library_set59/set1/D8.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set59/set1/C3.png	RNA_Library_set59/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-23	BGRSLV04-24
RBP	NDUFS6	NDUFS6
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	3560	3561

Sequencing Information

	BGRSLV04-23	BGRSLV04-24
Sample_ID	BGRSLV04-23	BGRSLV04-24
Sample Name	NDUFS6-BGRSLV04-23	NDUFS6-BGRSLV04-24
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	47,508,164	46,640,395
total_aligned_reads	39,725,591	39,358,749
unique_aligned_reads	36,736,791	36,320,852
percent_uniqueAligned	0.77327	0.77874
correlation_replicates	0.996765	0.996765
spikein_reads	321,270	217,652
percent_spikeins	0.00676	0.00467
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2431	2432

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
NDUFS6-BGRSLV04-23_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2431	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	8058
NDUFS6-BGRSLV04-23_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2431	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	8096
NDUFS6-BGRSLV04-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2431					GRCh38	V40	NDUFS6-BGRSLV04-23_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,NDUFS6-BGRSLV04-23_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11027
NDUFS6-BGRSLV04-23_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	2431					GRCh38	V40	NDUFS6-BGRSLV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	11065
NDUFS6-BGRSLV04-23_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	2431					GRCh38	V40	NDUFS6-BGRSLV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	11103
NDUFS6-BGRSLV04-23_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	2431					GRCh38	V40	NDUFS6-BGRSLV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	11141
NDUFS6-BGRSLV04-23_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	2431					GRCh38	V40	NDUFS6-BGRSLV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	11179
NDUFS6-BGRSLV04-23_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2431					GRCh38	V40	NDUFS6-BGRSLV04-23_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,NDUFS6-BGRSLV04-23_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11217
NDUFS6-BGRSLV04-24_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2432	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	8059
NDUFS6-BGRSLV04-24_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2432	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	8097
NDUFS6-BGRSLV04-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2432					GRCh38	V40	NDUFS6-BGRSLV04-24_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,NDUFS6-BGRSLV04-24_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11028
NDUFS6-BGRSLV04-24_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	2432					GRCh38	V40	NDUFS6-BGRSLV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	11066
NDUFS6-BGRSLV04-24_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	2432					GRCh38	V40	NDUFS6-BGRSLV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	11104
NDUFS6-BGRSLV04-24_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	2432					GRCh38	V40	NDUFS6-BGRSLV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	11142
NDUFS6-BGRSLV04-24_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	2432					GRCh38	V40	NDUFS6-BGRSLV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	11180
NDUFS6-BGRSLV04-24_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2432					GRCh38	V40	NDUFS6-BGRSLV04-24_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,NDUFS6-BGRSLV04-24_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11218