non-target RNA-Seq in 293T

General Information

List KD experiments controlled by BG293LV03-1 and BG293LV03-2

NT-BG293LV03-1,NT-BG293LV03-2:

BL-BG293LV03-WT293

DDX17-BG293LV03-WT293

RNPS1-BG293LV03-WT293

TOB2-BG293LV03-WT293

TRNAU1AP-BG293LV03-WT293

UBE2I-BG293LV03-WT293

ZC3HAV1-BG293LV03-WT293

Experiment Information (Status: Submitting)

	BG293LV03-1	BG293LV03-2
idx	0	0
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BG293LV03-1	BG293LV03-2
transduction_Date	4/10/23	4/10/23
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	9851	9852

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-1	BG293LV03-2
Sample_ID	BG293LV03-1	BG293LV03-2
Sample Name
Sample Name	NT-BG293LV03-1	NT-BG293LV03-2
RBP	non-target	non-target
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11738	11739

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-1	BG293LV03-2
Sample #	1	2
Sample Name	NT-BG293LV03-1	NT-BG293LV03-2
Sample_Name_Alias
Index Well Position	A01	B01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	279	296
Peak_Molarity	11.90	39.80
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A1.png	DNA_Library_set60-62/set4/B1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A1.png	RNA_Library_set60-62/set2/B1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-1	BG293LV03-2
RBP	NT	NT
Batch_ID	BG293LV03	BG293LV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3684	3685

Sequencing Information

	BG293LV03-1	BG293LV03-2
Sample_ID	BG293LV03-1	BG293LV03-2
Sample Name	NT-BG293LV03-1	NT-BG293LV03-2
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	35,673,212	40,344,128
total_aligned_reads	18,378,936	34,549,320
unique_aligned_reads	17,225,857	32,364,537
percent_uniqueAligned	0.48288	0.80221
correlation_replicates	0.976857	0.976857
spikein_reads	112,062	159,752
percent_spikeins	0.00314	0.00396
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2555	2556

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-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2555	NovaSeq6000	100	paired-ended	1				ENCORE2	7846
NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2555	NovaSeq6000	100	paired-ended	2				ENCORE2	7862
NT-BG293LV03-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2555					GRCh38	V40	NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10087
NT-BG293LV03-1_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2555					GRCh38	V40	NT-BG293LV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	10103
NT-BG293LV03-1_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2555					GRCh38	V40	NT-BG293LV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	10119
NT-BG293LV03-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2555					GRCh38	V40	NT-BG293LV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	10135
NT-BG293LV03-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2555					GRCh38	V40	NT-BG293LV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	10151
NT-BG293LV03-1_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2555					GRCh38	V40	NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10167
NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2556	NovaSeq6000	100	paired-ended	1				ENCORE2	7847
NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2556	NovaSeq6000	100	paired-ended	2				ENCORE2	7863
NT-BG293LV03-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2556					GRCh38	V40	NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10088
NT-BG293LV03-2_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2556					GRCh38	V40	NT-BG293LV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	10104
NT-BG293LV03-2_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2556					GRCh38	V40	NT-BG293LV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	10120
NT-BG293LV03-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2556					GRCh38	V40	NT-BG293LV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	10136
NT-BG293LV03-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2556					GRCh38	V40	NT-BG293LV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	10152
NT-BG293LV03-2_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2556					GRCh38	V40	NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10168