SRP72 RNA-Seq in K562

General Information


RBP	SRP72
Cell_Line	K562
Method	CRISPR
Exp_Name	SRP72-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SRP72-BGKcLV37-35
Rep2	SRP72-BGKcLV37-36
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	66.5
Rep2_qPCR	66.0
Rep1_WB	60.9
Rep2_WB	54.1
Antibody Cat#	A304-594A
Antibody Lot#	lot # 1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1057

Experiment Information (Status: Submitting)

	BGKcLV37-35	BGKcLV37-36
idx	1387	1388
TRCN#_or_BGC#	BGC#0001050	BGC#0001050
shRNA_or_gRNA_sequence	GGGTGTCAGTACCTGCGCTG	GGGTGTCAGTACCTGCGCTG
PAM	TGG	TGG
Name	SRP72_82	SRP72_82
Sample_ID	BGKcLV37-35	BGKcLV37-36
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	SRP72	SRP72
qPCR_result	66.5	66.0
Ave_qPCR	66.3
RT-qPCR_primer-F	tcaaatatgggcggaagaag
RT-qPCR_primer-R	aataagctgtgccagggtgt
protein_conc	1671	1627
WB_result	60.9	54.1
Ave_WB	57.5
WB_DONE_date	9/29/22	Licor
MW	75kd
IP
antibody_Cat#	A304-594A	lot # 1
Antibody DCC ID	NO ID
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5539	5540

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRP72	Product_ID: A304-594A Lot_ID: 1 Source: Bethyl Labs Target Name: SRP72-human

Experiment Status

	BGKcLV37-35	BGKcLV37-36
Sample_ID	BGKcLV37-35	BGKcLV37-36
Sample Name
Sample Name	SRP72-BGKcLV37-35	SRP72-BGKcLV37-36
RBP	SRP72	SRP72
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11098	11099

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-35	BGKcLV37-36
Sample #	37	38
Sample Name	SRP72-BGKcLV37-35	SRP72-BGKcLV37-36
Sample_Name_Alias
Index Well Position	E05	F05
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	299	302
Peak_Molarity	41.30	53.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/E5.png	DNA_Library_set54-56/set1/F5.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set54-56/set1/E5.png	RNA_Library_set54-56/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-35	BGKcLV37-36
RBP	SRP72	SRP72
Batch_ID	BGKcLV37	BGKcLV37
WB_result	60.900	54.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3408	3409

Sequencing Information

	BGKcLV37-35	BGKcLV37-36
Sample_ID	BGKcLV37-35	BGKcLV37-36
Sample Name	SRP72-BGKcLV37-35	SRP72-BGKcLV37-36
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	55,106,495	47,694,550
total_aligned_reads	51,454,409	45,137,044
unique_aligned_reads	47,802,739	41,800,625
percent_uniqueAligned	0.86746	0.87642
correlation_replicates	0.997781	0.997781
spikein_reads	2,602	2,730
percent_spikeins	0.00005	0.00006
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2281	2282

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	controlled_by	Project	FILE_ID
SRP72-BGKcLV37-35_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2281	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8402
SRP72-BGKcLV37-35_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2281	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8452
SRP72-BGKcLV37-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2281					GRCh38	V40	SRP72-BGKcLV37-35_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP72-BGKcLV37-35_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25643
SRP72-BGKcLV37-35_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	2281					GRCh38	V40	SRP72-BGKcLV37-35/Aligned.sortedByCoord.out.bam		ENCORE2	25693
SRP72-BGKcLV37-35_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	2281					GRCh38	V40	SRP72-BGKcLV37-35/Aligned.sortedByCoord.out.bam		ENCORE2	25743
SRP72-BGKcLV37-35_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	2281					GRCh38	V40	SRP72-BGKcLV37-35/Aligned.sortedByCoord.out.bam		ENCORE2	25793
SRP72-BGKcLV37-35_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	2281					GRCh38	V40	SRP72-BGKcLV37-35/Aligned.sortedByCoord.out.bam		ENCORE2	25843
SRP72-BGKcLV37-35_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2281					GRCh38	V40	SRP72-BGKcLV37-35_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP72-BGKcLV37-35_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25893
SRP72-BGKcLV37-36_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2282	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8403
SRP72-BGKcLV37-36_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2282	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8453
SRP72-BGKcLV37-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2282					GRCh38	V40	SRP72-BGKcLV37-36_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP72-BGKcLV37-36_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25644
SRP72-BGKcLV37-36_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	2282					GRCh38	V40	SRP72-BGKcLV37-36/Aligned.sortedByCoord.out.bam		ENCORE2	25694
SRP72-BGKcLV37-36_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	2282					GRCh38	V40	SRP72-BGKcLV37-36/Aligned.sortedByCoord.out.bam		ENCORE2	25744
SRP72-BGKcLV37-36_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	2282					GRCh38	V40	SRP72-BGKcLV37-36/Aligned.sortedByCoord.out.bam		ENCORE2	25794
SRP72-BGKcLV37-36_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	2282					GRCh38	V40	SRP72-BGKcLV37-36/Aligned.sortedByCoord.out.bam		ENCORE2	25844
SRP72-BGKcLV37-36_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2282					GRCh38	V40	SRP72-BGKcLV37-36_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP72-BGKcLV37-36_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25894