SRPRB RNA-Seq in K562

General Information


RBP	SRPRB
Cell_Line	K562
Method	CRISPR
Exp_Name	SRPRB-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	SRPRB-BGKcLV37-43
Rep2	SRPRB-BGKcLV37-44
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	48.0
Rep2_qPCR	48.1
Rep1_WB	61.8
Rep2_WB	65.2
Antibody Cat#	A305-440A
Antibody Lot#	lot # 1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1060

Experiment Information (Status: Submitting)

	BGKcLV37-43	BGKcLV37-44
idx	1395	1396
TRCN#_or_BGC#	BGC#0001059	BGC#0001059
shRNA_or_gRNA_sequence	TTCCGCGGACTCGCGCCGGG	TTCCGCGGACTCGCGCCGGG
PAM	TGG	TGG
Name	SRPRB_93B	SRPRB_93B
Sample_ID	BGKcLV37-43	BGKcLV37-44
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	SRPRB	SRPRB
qPCR_result	48.0	48.1
Ave_qPCR	48.0
RT-qPCR_primer-F	tcagacgtccattactgacagc
RT-qPCR_primer-R	tgaagcctcaaactctcatgg
protein_conc	1497	1579
WB_result	61.8	65.2
Ave_WB	63.5
WB_DONE_date	9/27/22	Licor
MW	30kd
IP	Rabbit / I
antibody_Cat#	A305-440A	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	5551	5552

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRPRB	Product_ID: A305-440A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPRB-human

Experiment Status

	BGKcLV37-43	BGKcLV37-44
Sample_ID	BGKcLV37-43	BGKcLV37-44
Sample Name
Sample Name	SRPRB-BGKcLV37-43	SRPRB-BGKcLV37-44
RBP	SRPRB	SRPRB
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11104	11105

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-43	BGKcLV37-44
Sample #	43	44
Sample Name	SRPRB-BGKcLV37-43	SRPRB-BGKcLV37-44
Sample_Name_Alias
Index Well Position	C06	D06
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	305	305
Peak_Molarity	68.60	57.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/C6.png	DNA_Library_set54-56/set1/D6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/C6.png	RNA_Library_set54-56/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-43	BGKcLV37-44
RBP	SRPRB	SRPRB
Batch_ID	BGKcLV37	BGKcLV37
WB_result	61.800	65.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3414	3415

Sequencing Information

	BGKcLV37-43	BGKcLV37-44
Sample_ID	BGKcLV37-43	BGKcLV37-44
Sample Name	SRPRB-BGKcLV37-43	SRPRB-BGKcLV37-44
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	57,282,929	51,796,936
total_aligned_reads	54,956,712	49,161,476
unique_aligned_reads	51,022,202	45,783,598
percent_uniqueAligned	0.89071	0.88391
correlation_replicates	0.997755	0.997755
spikein_reads	4,842	3,518
percent_spikeins	0.00008	0.00007
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2287	2288

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
SRPRB-BGKcLV37-43_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2287	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	8416
SRPRB-BGKcLV37-43_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2287	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	8466
SRPRB-BGKcLV37-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2287					GRCh38	V40	SRPRB-BGKcLV37-43_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGKcLV37-43_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25657
SRPRB-BGKcLV37-43_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	2287					GRCh38	V40	SRPRB-BGKcLV37-43/Aligned.sortedByCoord.out.bam		ENCORE2	25707
SRPRB-BGKcLV37-43_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	2287					GRCh38	V40	SRPRB-BGKcLV37-43/Aligned.sortedByCoord.out.bam		ENCORE2	25757
SRPRB-BGKcLV37-43_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	2287					GRCh38	V40	SRPRB-BGKcLV37-43/Aligned.sortedByCoord.out.bam		ENCORE2	25807
SRPRB-BGKcLV37-43_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	2287					GRCh38	V40	SRPRB-BGKcLV37-43/Aligned.sortedByCoord.out.bam		ENCORE2	25857
SRPRB-BGKcLV37-43_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2287					GRCh38	V40	SRPRB-BGKcLV37-43_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGKcLV37-43_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25907
SRPRB-BGKcLV37-44_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2288	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	8417
SRPRB-BGKcLV37-44_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2288	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	8467
SRPRB-BGKcLV37-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2288					GRCh38	V40	SRPRB-BGKcLV37-44_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGKcLV37-44_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25658
SRPRB-BGKcLV37-44_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	2288					GRCh38	V40	SRPRB-BGKcLV37-44/Aligned.sortedByCoord.out.bam		ENCORE2	25708
SRPRB-BGKcLV37-44_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	2288					GRCh38	V40	SRPRB-BGKcLV37-44/Aligned.sortedByCoord.out.bam		ENCORE2	25758
SRPRB-BGKcLV37-44_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	2288					GRCh38	V40	SRPRB-BGKcLV37-44/Aligned.sortedByCoord.out.bam		ENCORE2	25808
SRPRB-BGKcLV37-44_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	2288					GRCh38	V40	SRPRB-BGKcLV37-44/Aligned.sortedByCoord.out.bam		ENCORE2	25858
SRPRB-BGKcLV37-44_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2288					GRCh38	V40	SRPRB-BGKcLV37-44_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGKcLV37-44_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25908