non-target RNA-Seq in K562

General Information

List KD experiments controlled by BGKcLV37-1 and BGKcLV37-2

NT-BGKcLV37-1,NT-BGKcLV37-2:

DDX5-BGKcLV37-K562

Experiment Information (Status: Submitting)

	BGKcLV37-1	BGKcLV37-2
idx	1353	1354
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	non-target	non-target
Sample_ID	BGKcLV37-1	BGKcLV37-2
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	1731
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	5503	5504

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV37-1	BGKcLV37-2
Sample_ID	BGKcLV37-1	BGKcLV37-2
Sample Name
Sample Name	NT-BGKcLV37-1	NT-BGKcLV37-2
RBP	non-target	non-target
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11082	11083

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-1	BGKcLV37-2
Sample #	21	22
Sample Name	NT-BGKcLV37-1	NT-BGKcLV37-2
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	300	302
Peak_Molarity	54.50	65.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/E3.png	DNA_Library_set54-56/set1/F3.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/E3.png	RNA_Library_set54-56/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-1	BGKcLV37-2
RBP	NT	NT
Batch_ID	BGKcLV37	BGKcLV37
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3392	3393

Sequencing Information

	BGKcLV37-1	BGKcLV37-2
Sample_ID	BGKcLV37-1	BGKcLV37-2
Sample Name	NT-BGKcLV37-1	NT-BGKcLV37-2
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	53,853,855	42,194,520
total_aligned_reads	47,706,429	39,823,161
unique_aligned_reads	44,237,763	36,997,442
percent_uniqueAligned	0.82144	0.87683
correlation_replicates	0.997545	0.997545
spikein_reads	2,542	4,170
percent_spikeins	0.00005	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2265	2266

Data Submission Information DCC submission information was not avaliable

File Information

Search:

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-BGKcLV37-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2265					GRCh38	V40	NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	25629
NT-BGKcLV37-1_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2265					GRCh38	V40	NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	25879
NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2265	NovaSeq6000	100	paired-ended	1				ENCORE2	8388
NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2265	NovaSeq6000	100	paired-ended	2				ENCORE2	8438
NT-BGKcLV37-1_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2265					GRCh38	V40	NT-BGKcLV37-1/Aligned.sortedByCoord.out.bam	ENCORE2	25679
NT-BGKcLV37-1_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2265					GRCh38	V40	NT-BGKcLV37-1/Aligned.sortedByCoord.out.bam	ENCORE2	25729
NT-BGKcLV37-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2265					GRCh38	V40	NT-BGKcLV37-1/Aligned.sortedByCoord.out.bam	ENCORE2	25779
NT-BGKcLV37-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2265					GRCh38	V40	NT-BGKcLV37-1/Aligned.sortedByCoord.out.bam	ENCORE2	25829
NT-BGKcLV37-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2266					GRCh38	V40	NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	25630
NT-BGKcLV37-2_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2266					GRCh38	V40	NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	25880
NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2266	NovaSeq6000	100	paired-ended	1				ENCORE2	8389
NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2266	NovaSeq6000	100	paired-ended	2				ENCORE2	8439
NT-BGKcLV37-2_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2266					GRCh38	V40	NT-BGKcLV37-2/Aligned.sortedByCoord.out.bam	ENCORE2	25680
NT-BGKcLV37-2_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2266					GRCh38	V40	NT-BGKcLV37-2/Aligned.sortedByCoord.out.bam	ENCORE2	25730
NT-BGKcLV37-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2266					GRCh38	V40	NT-BGKcLV37-2/Aligned.sortedByCoord.out.bam	ENCORE2	25780
NT-BGKcLV37-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2266					GRCh38	V40	NT-BGKcLV37-2/Aligned.sortedByCoord.out.bam	ENCORE2	25830

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