SRPK1 RNA-Seq in HepG2

General Information


RBP	SRPK1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRPK1-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	SRPK1-BGHcLV36-37
Rep2	SRPK1-BGHcLV36-38
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	71.6
Rep2_qPCR	63.7
Rep1_WB	85.0
Rep2_WB	79.0
Antibody Cat#	A302-461A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1044

Experiment Information (Status: Submitting)

	BGHcLV36-37	BGHcLV36-38
idx	1168	1169
TRCN#_or_BGC#	BGC#0001055	BGC#0001055
shRNA_or_gRNA_sequence	AGCCTAACTTTCGGATCACA	AGCCTAACTTTCGGATCACA
PAM	TGG	TGG
Name	SRPK1_91	SRPK1_91
Sample_ID	BGHcLV36-37	BGHcLV36-38
transduction_Date	8/2/22	8/2/22
days	D6	D6
RBP_name	SRPK1	SRPK1
qPCR_result	71.6	63.7
Ave_qPCR	67.7
RT-qPCR_primer-F	gggcagagataccctgtgaa
RT-qPCR_primer-R	tggctcaaggggattaacaa
protein_conc	5557	5739
WB_result	85.0	79.0
Ave_WB	82.0
WB_DONE_date	9/14/22
MW	74kd
IP
antibody_Cat#	A302-461A	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	7349	7350

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRPK1	Product_ID: A302-462A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPK1-human

Experiment Status

	BGHcLV36-37	BGHcLV36-38
Sample_ID	BGHcLV36-37	BGHcLV36-38
Sample Name
Sample Name	SRPK1-BGHcLV36-37	SRPK1-BGHcLV36-38
RBP	SRPK1	SRPK1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10950	10951

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-37	BGHcLV36-38
Sample #	9	10
Sample Name	SRPK1-BGHcLV36-37	SRPK1-BGHcLV36-38
Sample_Name_Alias
Index Well Position	A02	B02
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	298	295
Peak_Molarity	28.60	41.80
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/A2.png	DNA_Library_set54-56/set1/B2.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/A2.png	RNA_Library_set54-56/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-37	BGHcLV36-38
RBP	SRPK1	SRPK1
Batch_ID	BGHcLV36	BGHcLV36
WB_result	85.000	79.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3380	3381

Sequencing Information

	BGHcLV36-37	BGHcLV36-38
Sample_ID	BGHcLV36-37	BGHcLV36-38
Sample Name	SRPK1-BGHcLV36-37	SRPK1-BGHcLV36-38
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	36,069,993	74,017,201
total_aligned_reads	33,663,809	67,262,831
unique_aligned_reads	31,929,578	63,667,741
percent_uniqueAligned	0.88521	0.86017
correlation_replicates	0.992745	0.992745
spikein_reads	8,488	11,908
percent_spikeins	0.00024	0.00016
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2253	2254

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
SRPK1-BGHcLV36-37_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2253	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	8406
SRPK1-BGHcLV36-37_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2253	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	8456
SRPK1-BGHcLV36-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2253					GRCh38	V40	SRPK1-BGHcLV36-37_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGHcLV36-37_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25647
SRPK1-BGHcLV36-37_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	2253					GRCh38	V40	SRPK1-BGHcLV36-37/Aligned.sortedByCoord.out.bam		ENCORE2	25697
SRPK1-BGHcLV36-37_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	2253					GRCh38	V40	SRPK1-BGHcLV36-37/Aligned.sortedByCoord.out.bam		ENCORE2	25747
SRPK1-BGHcLV36-37_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	2253					GRCh38	V40	SRPK1-BGHcLV36-37/Aligned.sortedByCoord.out.bam		ENCORE2	25797
SRPK1-BGHcLV36-37_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	2253					GRCh38	V40	SRPK1-BGHcLV36-37/Aligned.sortedByCoord.out.bam		ENCORE2	25847
SRPK1-BGHcLV36-37_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2253					GRCh38	V40	SRPK1-BGHcLV36-37_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGHcLV36-37_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25897
SRPK1-BGHcLV36-38_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2254	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	8407
SRPK1-BGHcLV36-38_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2254	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	8457
SRPK1-BGHcLV36-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2254					GRCh38	V40	SRPK1-BGHcLV36-38_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGHcLV36-38_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25648
SRPK1-BGHcLV36-38_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	2254					GRCh38	V40	SRPK1-BGHcLV36-38/Aligned.sortedByCoord.out.bam		ENCORE2	25698
SRPK1-BGHcLV36-38_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	2254					GRCh38	V40	SRPK1-BGHcLV36-38/Aligned.sortedByCoord.out.bam		ENCORE2	25748
SRPK1-BGHcLV36-38_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	2254					GRCh38	V40	SRPK1-BGHcLV36-38/Aligned.sortedByCoord.out.bam		ENCORE2	25798
SRPK1-BGHcLV36-38_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	2254					GRCh38	V40	SRPK1-BGHcLV36-38/Aligned.sortedByCoord.out.bam		ENCORE2	25848
SRPK1-BGHcLV36-38_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2254					GRCh38	V40	SRPK1-BGHcLV36-38_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGHcLV36-38_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25898