non-target RNA-Seq in 293T

General Information

List KD experiments controlled by BG293LV04-1 and BG293LV04-2

NT-BG293LV04-1,NT-BG293LV04-2:

PRRC2B-BG293LV04-WT293

CDC40-BG293LV04-WT293

DDX5-BG293LV04-WT293

HNRNPCL1-BG293LV04-WT293

HNRNPH1-BG293LV04-WT293

NUDT21-BG293LV04-WT293

PCBP3-BG293LV04-WT293

PPIA-BG293LV04-WT293

RBM11-BG293LV04-WT293

RBM4-BG293LV04-WT293

RBM5-BG293LV04-WT293

SCAF8-BG293LV04-WT293

SRP68-BG293LV04-WT293

Experiment Information (Status: Submitting)

	BG293LV04-1	BG293LV04-2
idx	0	0
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	non-target	non-target
Sample_ID	BG293LV04-1	BG293LV04-2
transduction_Date	9/7/23	9/7/23
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	9888	9889

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-1	BG293LV04-2
Sample_ID	BG293LV04-1	BG293LV04-2
Sample Name
Sample Name	NT-BG293LV04-1	NT-BG293LV04-2
RBP	non-target	non-target
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12514	12515

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-1	BG293LV04-2
Sample #	1	2
Sample Name	NT-BG293LV04-1	NT-BG293LV04-2
Sample_Name_Alias
Index Well Position	A01	B01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	282	278
Peak_Molarity	70.20	78.70
libSampleQC_DNA_Well	DNA_Library_set64/set1/A9.png	DNA_Library_set64/set1/B9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set64/set1/A5.png	RNA_Library_set64/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-1	BG293LV04-2
RBP	NT	NT
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4006	4007

Sequencing Information

	BG293LV04-1	BG293LV04-2
Sample_ID	BG293LV04-1	BG293LV04-2
Sample Name	NT-BG293LV04-1	NT-BG293LV04-2
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	23,445,406	24,749,165
total_aligned_reads	20,991,664	22,741,028
unique_aligned_reads	19,453,272	21,141,146
percent_uniqueAligned	0.82973	0.85422
correlation_replicates	0.995581	0.995581
spikein_reads	22,626	11,532
percent_spikeins	0.00097	0.00047
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2615	2616

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-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2615	NextSeq2000	100	paired-ended	1				ENCORE2	8690
NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2615	NextSeq2000	100	paired-ended	2				ENCORE2	8718
NT-BG293LV04-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2615					GRCh38	V40	NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9767
NT-BG293LV04-1_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2615					GRCh38	V40	NT-BG293LV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	9795
NT-BG293LV04-1_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2615					GRCh38	V40	NT-BG293LV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	9823
NT-BG293LV04-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2615					GRCh38	V40	NT-BG293LV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	9851
NT-BG293LV04-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2615					GRCh38	V40	NT-BG293LV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	9879
NT-BG293LV04-1_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2615					GRCh38	V40	NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9907
NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2616	NextSeq2000	100	paired-ended	1				ENCORE2	8691
NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2616	NextSeq2000	100	paired-ended	2				ENCORE2	8719
NT-BG293LV04-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2616					GRCh38	V40	NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9768
NT-BG293LV04-2_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2616					GRCh38	V40	NT-BG293LV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	9796
NT-BG293LV04-2_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2616					GRCh38	V40	NT-BG293LV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	9824
NT-BG293LV04-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2616					GRCh38	V40	NT-BG293LV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	9852
NT-BG293LV04-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2616					GRCh38	V40	NT-BG293LV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	9880
NT-BG293LV04-2_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2616					GRCh38	V40	NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9908