non-target RNA-Seq in 293T

General Information

List KD experiments controlled by BG293LV06-37 and BG293LV06-38

NT-BG293LV06-37,NT-BG293LV06-38:No KD experiments controlled by NT-BG293LV06-37 and NT-BG293LV06-38 are available on the database

NT-BG293LV06-37B,NT-BG293LV06-38B:No KD experiments controlled by NT-BG293LV06-37B and NT-BG293LV06-38B are available on the database

NT-BG293LV06-37C,NT-BG293LV06-38C:No KD experiments controlled by NT-BG293LV06-37C and NT-BG293LV06-38C are available on the database

Experiment Information (Status: Released)

	BG293LV06-37	BG293LV06-38
idx	0	0
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	non-target	non-target
Sample_ID	BG293LV06-37	BG293LV06-38
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	12172	12173

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-37	BG293LV06-37	BG293LV06-37	BG293LV06-38	BG293LV06-38	BG293LV06-38
Sample_ID	BG293LV06-37	BG293LV06-37	BG293LV06-37	BG293LV06-38	BG293LV06-38	BG293LV06-38
Sample Name
Sample Name	NT-BG293LV06-37	NT-BG293LV06-37	NT-BG293LV06-37	NT-BG293LV06-38	NT-BG293LV06-38	NT-BG293LV06-38
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	13474	13566	13574	13475	13567	13575

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-37	BG293LV06-37	BG293LV06-37	BG293LV06-38	BG293LV06-38	BG293LV06-38
Sample #	3	129	3	4	130	4
Sample Name	NT-BG293LV06-37	NT-BG293LV06-37B	NT-BG293LV06-37C	NT-BG293LV06-38	NT-BG293LV06-38B	NT-BG293LV06-38C
Sample_Name_Alias
Index Well Position	C01	C01	C10	D01	D01	D10
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	291	271	298	283	274	293
Peak_Molarity	71.90	77.90	99.30	94.70	104.00	85.40
libSampleQC_DNA_Well	DNA_Library_set71/set1/C1.png	DNA_Library_set72/set1/C1.png	DNA_Library_set72/set1/C1.png	DNA_Library_set71/set1/D1.png	DNA_Library_set72/set1/D1.png	DNA_Library_set72/set1/D1.png
RIN	10.0	10.0	10.0	10.0	9.9	9.9
libSample_RNA_Well	RNA_Library_set71/set1/C1.png	RNA_Library_set72/set1/C1.png	RNA_Library_set72/set1/C1.png	RNA_Library_set71/set1/D1.png	RNA_Library_set72/set1/D1.png	RNA_Library_set72/set1/D1.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	BG293LV06-37	BG293LV06-37	BG293LV06-37	BG293LV06-38	BG293LV06-38	BG293LV06-38
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	4428	4554	4562	4429	4555	4563

Sequencing Information

	BG293LV06-37	BG293LV06-37	BG293LV06-37	BG293LV06-38	BG293LV06-38	BG293LV06-38
Sample_ID	BG293LV06-37	BG293LV06-37	BG293LV06-37	BG293LV06-38	BG293LV06-38	BG293LV06-38
Sample Name	NT-BG293LV06-37	NT-BG293LV06-37B	NT-BG293LV06-37C	NT-BG293LV06-38	NT-BG293LV06-38B	NT-BG293LV06-38C
Pool ID	Pool-240930	Pool-241004	Pool-241004	Pool-240930	Pool-241004	Pool-241004
LocalServer_folder	set71	set72	set72	set71	set72	set72
total_reads	21,073,534	15,053,324	23,031,111	28,953,572	31,448,397	25,050,664
total_aligned_reads	18,502,162	12,126,680	21,459,812	26,103,050	28,146,444	23,329,909
unique_aligned_reads	17,339,374	11,277,894	19,952,402	24,334,156	26,226,030	21,652,874
percent_uniqueAligned	0.82280	0.74920	0.86632	0.84045	0.83394	0.86436
correlation_replicates	0.947003	0.995918	0.991845	0.947003	0.995918	0.991845
spikein_reads	61,274	15,802	55,954	94,908	75,406	46,392
percent_spikeins	0.00291	0.00105	0.00243	0.00328	0.00240	0.00185
original_ReadLength	101	101	101	101	101	101
QC_Status	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted
ID	2997	3123	3131	2998	3124	3132

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-BG293LV06-37_S3_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2997	NovaSeq6000	100	paired-ended	1				ENCORE2	29341
NT-BG293LV06-37_S3_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2997	NovaSeq6000	100	paired-ended	2				ENCORE2	29405
NT-BG293LV06-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2997					GRCh38	V40	NT-BG293LV06-37_S3_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-37_S3_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29470
NT-BG293LV06-37_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	2997					GRCh38	V40	NT-BG293LV06-37_Aligned.sortedByCoord.out.bam	ENCORE2	29534
NT-BG293LV06-37_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	2997					GRCh38	V40	NT-BG293LV06-37_Aligned.sortedByCoord.out.bam	ENCORE2	29598
NT-BG293LV06-37_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	2997					GRCh38	V40	NT-BG293LV06-37_Aligned.sortedByCoord.out.bam	ENCORE2	29662
NT-BG293LV06-37_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2997					GRCh38	V40	NT-BG293LV06-37_S3_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-37_S3_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29726
NT-BG293LV06-37B_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3123	NovaSeq6000	100	paired-ended	1				ENCORE2	29798
NT-BG293LV06-37B_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3123	NovaSeq6000	100	paired-ended	2				ENCORE2	29870
NT-BG293LV06-37B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3123					GRCh38	V40	NT-BG293LV06-37B_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-37B_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29942
NT-BG293LV06-37B_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	3123					GRCh38	V40	NT-BG293LV06-37B_Aligned.sortedByCoord.out.bam	ENCORE2	30014
NT-BG293LV06-37B_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	3123					GRCh38	V40	NT-BG293LV06-37B_Aligned.sortedByCoord.out.bam	ENCORE2	30086
NT-BG293LV06-37B_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	3123					GRCh38	V40	NT-BG293LV06-37B_Aligned.sortedByCoord.out.bam	ENCORE2	30158
NT-BG293LV06-37B_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	3123					GRCh38	V40	NT-BG293LV06-37B_Aligned.sortedByCoord.out.bam	ENCORE2	30230
NT-BG293LV06-37B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3123					GRCh38	V40	NT-BG293LV06-37B_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-37B_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30302
NT-BG293LV06-38_S4_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2998	NovaSeq6000	100	paired-ended	1				ENCORE2	29342
NT-BG293LV06-38_S4_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2998	NovaSeq6000	100	paired-ended	2				ENCORE2	29406
NT-BG293LV06-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2998					GRCh38	V40	NT-BG293LV06-38_S4_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-38_S4_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29471
NT-BG293LV06-38_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	2998					GRCh38	V40	NT-BG293LV06-38_Aligned.sortedByCoord.out.bam	ENCORE2	29535
NT-BG293LV06-38_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	2998					GRCh38	V40	NT-BG293LV06-38_Aligned.sortedByCoord.out.bam	ENCORE2	29599
NT-BG293LV06-38_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	2998					GRCh38	V40	NT-BG293LV06-38_Aligned.sortedByCoord.out.bam	ENCORE2	29663
NT-BG293LV06-38_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2998					GRCh38	V40	NT-BG293LV06-38_S4_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-38_S4_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29727
NT-BG293LV06-38B_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3124	NovaSeq6000	100	paired-ended	1				ENCORE2	29799
NT-BG293LV06-38B_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3124	NovaSeq6000	100	paired-ended	2				ENCORE2	29871
NT-BG293LV06-38B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3124					GRCh38	V40	NT-BG293LV06-38B_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-38B_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29943
NT-BG293LV06-38B_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	3124					GRCh38	V40	NT-BG293LV06-38B_Aligned.sortedByCoord.out.bam	ENCORE2	30015
NT-BG293LV06-38B_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	3124					GRCh38	V40	NT-BG293LV06-38B_Aligned.sortedByCoord.out.bam	ENCORE2	30087
NT-BG293LV06-38B_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	3124					GRCh38	V40	NT-BG293LV06-38B_Aligned.sortedByCoord.out.bam	ENCORE2	30159
NT-BG293LV06-38B_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	3124					GRCh38	V40	NT-BG293LV06-38B_Aligned.sortedByCoord.out.bam	ENCORE2	30231
NT-BG293LV06-38B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3124					GRCh38	V40	NT-BG293LV06-38B_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-38B_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30303