SRPK2 RNA-Seq in HepG2

General Information


RBP	SRPK2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRPK2-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR740LSP
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR929EIP
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	SRPK2-BGHcLV12-69
Rep2	SRPK2-BGHcLV12-70
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	73.6
Rep2_qPCR	77.3
Rep1_WB	92.9
Rep2_WB	89.0
Antibody Cat#	A302-467A
Antibody Lot#
Antibody DCC ID	ENCAB237YZZ
Status	Released
Project	ENCODE4
ID	191

Experiment Information (Status: Released)

	BGHcLV12-69	BGHcLV12-70
idx	329	330
TRCN#_or_BGC#	BGC#0000284	BGC#0000284
shRNA_or_gRNA_sequence	GCATTATACGGAGACAGCCT	GCATTATACGGAGACAGCCT
PAM	TGG	TGG
Name	SRPK2_77	SRPK2_77
Sample_ID	BGHcLV12-69	BGHcLV12-70
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	SRPK2	SRPK2
qPCR_result	73.6	77.3
Ave_qPCR	75.5
RT-qPCR_primer-F	atgaccaggatggcgaatac
RT-qPCR_primer-R	ttcaccattgtcctttgcag
protein_conc	5183	5603
WB_result	92.9	89.0
Ave_WB	91.0
WB_DONE_date	8/24/18	WES
MW	78kda
IP
antibody_Cat#	A302-467A
Antibody DCC ID	ENCAB237YZZ
submitted_to_DCC_date	2/22/19
Rep1_TPM	11	0
Rep2_TPM	22	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6474	6475

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRPK2	Product_ID: A302-467A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPK2-human

Experiment Status

	BGHcLV12-69	BGHcLV12-70
Sample_ID	BGHcLV12-69	BGHcLV12-70
Sample Name	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-70
Sample Name	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-70
RBP	SRPK2	SRPK2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2813	2814

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-69	BGHcLV12-70
Sample #	43	44
Sample Name	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-70
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-C2	3-D2
Tecan	36.09	37.37
Tecan_date	2019-03-13	2019-03-13
Size_bp	301	305
Peak_Molarity	144.00	115.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/C6.png	DNA_Library_set42/set1/D6.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set42/set1/C6.png	RNA_Library_set42/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-69	BGHcLV12-70
RBP	SRPK2	SRPK2
Batch_ID	BGHcLV12	BGHcLV12
WB_result	92.900	89.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	43	44

Sequencing Information

	BGHcLV12-69	BGHcLV12-70
Sample_ID	BGHcLV12-69	BGHcLV12-70
Sample Name	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-70
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	34,587,426	121,327,614
total_aligned_reads	32,735,492	111,170,192
unique_aligned_reads	30,841,924	104,441,438
percent_uniqueAligned	0.89171	0.86082
correlation_replicates	0.994276	0.994276
spikein_reads	50,646	164,000
percent_spikeins	0.00146	0.00135
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	69	70

Data Submission Information

	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-70	BGHcLV12-70	BGHcLV12-70	BGHcLV12-70
ENCODE_alias	brenton-graveley:SRPK2-BGHcLV12	brenton-graveley:SRPK2-BGHcLV12-69	brenton-graveley:L-SRPK2-BGHcLV12-69	brenton-graveley:SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRPK2-BGHcLV12-HepG2	brenton-graveley:SRPK2-BGHcLV12-70	brenton-graveley:L-SRPK2-BGHcLV12-70	brenton-graveley:SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR929EIP	ENCBS575STC	ENCLB908BWG	ENCFF731VGC	ENCFF401YAP	ENCSR740LSP	ENCBS139LMU	ENCLB896OQU	ENCFF496IVW	ENCFF866PXO
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-69	BGHcLV12-70	BGHcLV12-70	BGHcLV12-70	BGHcLV12-70
Sample Name	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-69	SRPK2-BGHcLV12-70	SRPK2-BGHcLV12-70	SRPK2-BGHcLV12-70	SRPK2-BGHcLV12-70
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		SRPK2-BGHcLV12-69.pdf	L-SRPK2-BGHcLV12-69.pdf				SRPK2-BGHcLV12-70.pdf	L-SRPK2-BGHcLV12-70.pdf
ID	753	801	883	1019	1101	7335	802	884	1020	1102

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
SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	69	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	401
SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	69	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	483
SRPK2-BGHcLV12-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	69					GRCh38	V40	SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23740
SRPK2-BGHcLV12-69_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	69					GRCh38	V40	SRPK2-BGHcLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	23822
SRPK2-BGHcLV12-69_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	69					GRCh38	V40	SRPK2-BGHcLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	23904
SRPK2-BGHcLV12-69_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	69					GRCh38	V40	SRPK2-BGHcLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	23986
SRPK2-BGHcLV12-69_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	69					GRCh38	V40	SRPK2-BGHcLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	24068
SRPK2-BGHcLV12-69_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	69					GRCh38	V40	SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRPK2-BGHcLV12-69_AAGATACT+ACTTACAT_HK3H2DSXX_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24150
SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	70	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	402
SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	70	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	484
SRPK2-BGHcLV12-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	70					GRCh38	V40	SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23741
SRPK2-BGHcLV12-70_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	70					GRCh38	V40	SRPK2-BGHcLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	23823
SRPK2-BGHcLV12-70_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	70					GRCh38	V40	SRPK2-BGHcLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	23905
SRPK2-BGHcLV12-70_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	70					GRCh38	V40	SRPK2-BGHcLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	23987
SRPK2-BGHcLV12-70_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	70					GRCh38	V40	SRPK2-BGHcLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	24069
SRPK2-BGHcLV12-70_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	70					GRCh38	V40	SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRPK2-BGHcLV12-70_GGAGCGTC+GTCCGTGC_HK3H2DSXX_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24151