SRPRB RNA-Seq in HepG2

General Information


RBP	SRPRB
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRPRB-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SRPRB-BGHcLV36-41
Rep2	SRPRB-BGHcLV36-42
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	60.1
Rep2_qPCR	69.9
Rep1_WB	74.7
Rep2_WB	64.9
Antibody Cat#	A305-440A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1046

Experiment Information (Status: Submitting)

	BGHcLV36-41	BGHcLV36-42
idx	1172	1173
TRCN#_or_BGC#	BGC#0001059	BGC#0001059
shRNA_or_gRNA_sequence	TTCCGCGGACTCGCGCCGGG	TTCCGCGGACTCGCGCCGGG
PAM	TGG	TGG
Name	SRPRB_93B	SRPRB_93B
Sample_ID	BGHcLV36-41	BGHcLV36-42
transduction_Date	8/2/22	8/2/22
days	D6	D6
RBP_name	SRPRB	SRPRB
qPCR_result	60.1	69.9
Ave_qPCR	65.0
RT-qPCR_primer-F	tcagacgtccattactgacagc
RT-qPCR_primer-R	tgaagcctcaaactctcatgg
protein_conc	3650	4728
WB_result	74.7	64.9
Ave_WB	69.8
WB_DONE_date	9/1/22
MW	30kd
IP	Rabbit / I
antibody_Cat#	A305-440A	lot # 1
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	7353	7354

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

	BGHcLV36-41	BGHcLV36-42
Sample_ID	BGHcLV36-41	BGHcLV36-42
Sample Name
Sample Name	SRPRB-BGHcLV36-41	SRPRB-BGHcLV36-42
RBP	SRPRB	SRPRB
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10954	10955

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-41	BGHcLV36-42
Sample #	13	14
Sample Name	SRPRB-BGHcLV36-41	SRPRB-BGHcLV36-42
Sample_Name_Alias
Index Well Position	E02	F02
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	295	300
Peak_Molarity	53.20	59.80
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/E2.png	DNA_Library_set54-56/set1/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set1/E2.png	RNA_Library_set54-56/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-41	BGHcLV36-42
RBP	SRPRB	SRPRB
Batch_ID	BGHcLV36	BGHcLV36
WB_result	74.700	64.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3384	3385

Sequencing Information

	BGHcLV36-41	BGHcLV36-42
Sample_ID	BGHcLV36-41	BGHcLV36-42
Sample Name	SRPRB-BGHcLV36-41	SRPRB-BGHcLV36-42
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	48,130,670	39,504,805
total_aligned_reads	43,757,963	35,998,177
unique_aligned_reads	41,532,099	34,151,867
percent_uniqueAligned	0.86290	0.86450
correlation_replicates	0.999098	0.999098
spikein_reads	2,232	3,770
percent_spikeins	0.00005	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2257	2258

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-BGHcLV36-41_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2257	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8414
SRPRB-BGHcLV36-41_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2257	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8464
SRPRB-BGHcLV36-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2257					GRCh38	V40	SRPRB-BGHcLV36-41_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGHcLV36-41_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25655
SRPRB-BGHcLV36-41_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	2257					GRCh38	V40	SRPRB-BGHcLV36-41/Aligned.sortedByCoord.out.bam		ENCORE2	25705
SRPRB-BGHcLV36-41_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	2257					GRCh38	V40	SRPRB-BGHcLV36-41/Aligned.sortedByCoord.out.bam		ENCORE2	25755
SRPRB-BGHcLV36-41_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	2257					GRCh38	V40	SRPRB-BGHcLV36-41/Aligned.sortedByCoord.out.bam		ENCORE2	25805
SRPRB-BGHcLV36-41_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	2257					GRCh38	V40	SRPRB-BGHcLV36-41/Aligned.sortedByCoord.out.bam		ENCORE2	25855
SRPRB-BGHcLV36-41_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2257					GRCh38	V40	SRPRB-BGHcLV36-41_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGHcLV36-41_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25905
SRPRB-BGHcLV36-42_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2258	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8415
SRPRB-BGHcLV36-42_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2258	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8465
SRPRB-BGHcLV36-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2258					GRCh38	V40	SRPRB-BGHcLV36-42_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGHcLV36-42_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25656
SRPRB-BGHcLV36-42_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	2258					GRCh38	V40	SRPRB-BGHcLV36-42/Aligned.sortedByCoord.out.bam		ENCORE2	25706
SRPRB-BGHcLV36-42_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	2258					GRCh38	V40	SRPRB-BGHcLV36-42/Aligned.sortedByCoord.out.bam		ENCORE2	25756
SRPRB-BGHcLV36-42_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	2258					GRCh38	V40	SRPRB-BGHcLV36-42/Aligned.sortedByCoord.out.bam		ENCORE2	25806
SRPRB-BGHcLV36-42_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	2258					GRCh38	V40	SRPRB-BGHcLV36-42/Aligned.sortedByCoord.out.bam		ENCORE2	25856
SRPRB-BGHcLV36-42_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2258					GRCh38	V40	SRPRB-BGHcLV36-42_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRB-BGHcLV36-42_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25906