non-target RNA-Seq in 293T

General Information

List KD experiments controlled by BG293LV06-73 and BG293LV06-74

NT-BG293LV06-73,NT-BG293LV06-74:No KD experiments controlled by NT-BG293LV06-73 and NT-BG293LV06-74 are available on the database

NT-BG293LV06-73B,NT-BG293LV06-74B:No KD experiments controlled by NT-BG293LV06-73B and NT-BG293LV06-74B are available on the database

NT-BG293LV06-73C,NT-BG293LV06-74C:No KD experiments controlled by NT-BG293LV06-73C and NT-BG293LV06-74C are available on the database

Experiment Information (Status: Released)

	BG293LV06-73	BG293LV06-74
idx	0	0
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	non-target	non-target
Sample_ID	BG293LV06-73	BG293LV06-74
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
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	12208	12209

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-73	BG293LV06-73	BG293LV06-73	BG293LV06-74	BG293LV06-74	BG293LV06-74
Sample_ID	BG293LV06-73	BG293LV06-73	BG293LV06-73	BG293LV06-74	BG293LV06-74	BG293LV06-74
Sample Name
Sample Name	NT-BG293LV06-73	NT-BG293LV06-73	NT-BG293LV06-73	NT-BG293LV06-74	NT-BG293LV06-74	NT-BG293LV06-74
RBP	non-target	non-target	non-target	non-target	non-target	non-target
Cell_Line	293T	293T	293T	293T	293T	293T
Exp UID
Status	Released	Released	Released	Released	Released	Released
Status_date	2025-04-21	2025-04-21	2025-04-21	2025-04-21	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13510	13568	13576	13511	13569	13577

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-73	BG293LV06-73	BG293LV06-73	BG293LV06-74	BG293LV06-74	BG293LV06-74
Sample #	5	131	5	6	132	6
Sample Name	NT-BG293LV06-73	NT-BG293LV06-73B	NT-BG293LV06-73C	NT-BG293LV06-74	NT-BG293LV06-74B	NT-BG293LV06-74C
Sample_Name_Alias
Index Well Position	E01	E01	E10	F01	F01	F10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-10-02	2024-10-02	2024-09-25	2024-10-02	2024-10-02
Lib_ID	Lib-240925B	Lib-241002	Lib-241002	Lib-240925B	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	301	275	283	281	286	284
Peak_Molarity	79.20	113.00	99.40	78.50	82.50	82.80
libSampleQC_DNA_Well	DNA_Library_set71/set1/E1.png	DNA_Library_set72/set1/E1.png	DNA_Library_set72/set1/E1.png	DNA_Library_set71/set1/F1.png	DNA_Library_set72/set1/F1.png	DNA_Library_set72/set1/F1.png
RIN	10.0	10.0	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_set71/set1/E1.png	RNA_Library_set72/set1/E1.png	RNA_Library_set72/set1/E1.png	RNA_Library_set71/set1/F1.png	RNA_Library_set72/set1/F1.png	RNA_Library_set72/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-10-04	2024-10-04	2024-09-30	2024-10-04	2024-10-04
Sample_ID	BG293LV06-73	BG293LV06-73	BG293LV06-73	BG293LV06-74	BG293LV06-74	BG293LV06-74
RBP	NT	NT	NT	NT	NT	NT
Batch_ID	BG293LV06	BG293LV06	BG293LV06	BG293LV06	BG293LV06	BG293LV06
WB_result	0.000	0.000	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B	C		B	C
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	4430	4556	4564	4431	4557	4565

Sequencing Information

	BG293LV06-73	BG293LV06-73	BG293LV06-73	BG293LV06-74	BG293LV06-74	BG293LV06-74
Sample_ID	BG293LV06-73	BG293LV06-73	BG293LV06-73	BG293LV06-74	BG293LV06-74	BG293LV06-74
Sample Name	NT-BG293LV06-73	NT-BG293LV06-73B	NT-BG293LV06-73C	NT-BG293LV06-74	NT-BG293LV06-74B	NT-BG293LV06-74C
Pool ID	Pool-240930	Pool-241004	Pool-241004	Pool-240930	Pool-241004	Pool-241004
LocalServer_folder	set71	set72	set72	set71	set72	set72
total_reads	32,342,825	47,723,253	26,042,546	23,182,988	24,255,673	22,202,552
total_aligned_reads	28,870,880	42,947,794	24,319,651	19,431,840	21,337,044	20,410,737
unique_aligned_reads	26,892,949	39,910,718	22,577,589	18,045,959	19,897,216	18,958,382
percent_uniqueAligned	0.83150	0.83630	0.86695	0.77841	0.82031	0.85388
correlation_replicates	0.995156	0.990906	0.992877	0.995156	0.990906	0.992877
spikein_reads	85,808	154,700	53,644	66,180	7,036	51,328
percent_spikeins	0.00265	0.00324	0.00206	0.00285	0.00029	0.00231
original_ReadLength	101	101	101	101	101	101
QC_Status	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted
ID	2999	3125	3133	3000	3126	3134

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	Project	FILE_ID
NT-BG293LV06-73_S5_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2999	NovaSeq6000	100	paired-ended	1				ENCORE2	29343
NT-BG293LV06-73_S5_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2999	NovaSeq6000	100	paired-ended	2				ENCORE2	29407
NT-BG293LV06-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2999					GRCh38	V40	NT-BG293LV06-73_S5_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-73_S5_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29472
NT-BG293LV06-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2999					GRCh38	V40	NT-BG293LV06-73_Aligned.sortedByCoord.out.bam	ENCORE2	29536
NT-BG293LV06-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2999					GRCh38	V40	NT-BG293LV06-73_Aligned.sortedByCoord.out.bam	ENCORE2	29600
NT-BG293LV06-73_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2999					GRCh38	V40	NT-BG293LV06-73_Aligned.sortedByCoord.out.bam	ENCORE2	29664
NT-BG293LV06-73_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2999					GRCh38	V40	NT-BG293LV06-73_S5_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-73_S5_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29728
NT-BG293LV06-73B_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3125	NovaSeq6000	100	paired-ended	1				ENCORE2	29800
NT-BG293LV06-73B_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3125	NovaSeq6000	100	paired-ended	2				ENCORE2	29872
NT-BG293LV06-73B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3125					GRCh38	V40	NT-BG293LV06-73B_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-73B_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29944
NT-BG293LV06-73B_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	3125					GRCh38	V40	NT-BG293LV06-73B_Aligned.sortedByCoord.out.bam	ENCORE2	30016
NT-BG293LV06-73B_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	3125					GRCh38	V40	NT-BG293LV06-73B_Aligned.sortedByCoord.out.bam	ENCORE2	30088
NT-BG293LV06-73B_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	3125					GRCh38	V40	NT-BG293LV06-73B_Aligned.sortedByCoord.out.bam	ENCORE2	30160
NT-BG293LV06-73B_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	3125					GRCh38	V40	NT-BG293LV06-73B_Aligned.sortedByCoord.out.bam	ENCORE2	30232
NT-BG293LV06-73B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3125					GRCh38	V40	NT-BG293LV06-73B_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-73B_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30304
NT-BG293LV06-74_S6_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3000	NovaSeq6000	100	paired-ended	1				ENCORE2	29344
NT-BG293LV06-74_S6_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3000	NovaSeq6000	100	paired-ended	2				ENCORE2	29408
NT-BG293LV06-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3000					GRCh38	V40	NT-BG293LV06-74_S6_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-74_S6_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29473
NT-BG293LV06-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3000					GRCh38	V40	NT-BG293LV06-74_Aligned.sortedByCoord.out.bam	ENCORE2	29537
NT-BG293LV06-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3000					GRCh38	V40	NT-BG293LV06-74_Aligned.sortedByCoord.out.bam	ENCORE2	29601
NT-BG293LV06-74_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3000					GRCh38	V40	NT-BG293LV06-74_Aligned.sortedByCoord.out.bam	ENCORE2	29665
NT-BG293LV06-74_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3000					GRCh38	V40	NT-BG293LV06-74_S6_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-74_S6_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29729
NT-BG293LV06-74B_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3126	NovaSeq6000	100	paired-ended	1				ENCORE2	29801
NT-BG293LV06-74B_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3126	NovaSeq6000	100	paired-ended	2				ENCORE2	29873
NT-BG293LV06-74B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3126					GRCh38	V40	NT-BG293LV06-74B_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-74B_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29945
NT-BG293LV06-74B_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	3126					GRCh38	V40	NT-BG293LV06-74B_Aligned.sortedByCoord.out.bam	ENCORE2	30017
NT-BG293LV06-74B_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	3126					GRCh38	V40	NT-BG293LV06-74B_Aligned.sortedByCoord.out.bam	ENCORE2	30089
NT-BG293LV06-74B_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	3126					GRCh38	V40	NT-BG293LV06-74B_Aligned.sortedByCoord.out.bam	ENCORE2	30161
NT-BG293LV06-74B_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	3126					GRCh38	V40	NT-BG293LV06-74B_Aligned.sortedByCoord.out.bam	ENCORE2	30233
NT-BG293LV06-74B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3126					GRCh38	V40	NT-BG293LV06-74B_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-74B_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30305