SRPK2 RNA-Seq in K562

General Information


RBP	SRPK2
Cell_Line	K562
Method	shRNA
Exp_Name	SRPK2-BGKLV34-K562
ENCODE_series_ID	ENCSR231HOJ
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR524YXQ
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	SRPK2_BGKLV34-39
Rep2	SRPK2_BGKLV34-40
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	45.5
Rep2_qPCR	43.0
Rep1_WB	91.4
Rep2_WB	93.3
Antibody Cat#	A302-467A
Antibody Lot#	A302-467A
Antibody DCC ID	ENCAB237YZZ
Status	Released
Project	ENCODE3
ID	726

Experiment Information (Status: Released)

	BGKLV34-39	BGKLV34-40
idx	702	703
TRCN#_or_BGC#	TRCN0000006277	TRCN0000006277
shRNA_or_gRNA_sequence	CGTTGTGTGAAGAGTATCATT	CGTTGTGTGAAGAGTATCATT
PAM
Name	SRPK2	SRPK2
Sample_ID	BGKLV34-39	BGKLV34-40
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	SRPK2	SRPK2
qPCR_result	45.5	43.0
Ave_qPCR	44.2
RT-qPCR_primer-F	agagcagtccatcccatgac
RT-qPCR_primer-R	caggggattcaccaacaagt
protein_conc	2065	2440
WB_result	91.4	93.3
Ave_WB	92.4
WB_DONE_date	2/11/2016
MW	78kDa	WES
IP	1	1
antibody_Cat#	A302-467A	A302-467A
Antibody DCC ID	ENCAB237YZZ	ENCAB237YZZ
submitted_to_DCC_date	3/8/2016
Rep1_TPM	67.66024464	0
Rep2_TPM	79.3941064	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	789	790

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

	BGKLV34-39	BGKLV34-40
Sample_ID	BGKLV34-39	BGKLV34-40
Sample Name	SRPK2_BGKLV34-39	SRPK2_BGKLV34-40
Sample Name	SRPK2_BGKLV34-39	SRPK2_BGKLV34-40
RBP	SRPK2	SRPK2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1241	1242

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-39	BGKLV34-40
Sample #
Sample Name	SRPK2-BGKLV34-39	SRPK2-BGKLV34-40
Sample_Name_Alias	SRPK2_BGKLV34-39	SRPK2_BGKLV34-40
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A4.png	DNA_Library_LV33-34-25B-32/set1/B4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/G5.png	RNA_Library_LV32-33-34/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-39	BGKLV34-40
RBP	SRPK2	SRPK2
Batch_ID	BGKLV34	BGKLV34
WB_result	91.400	93.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2926	2927

Sequencing Information

	BGKLV34-39	BGKLV34-40
Sample_ID	BGKLV34-39	BGKLV34-40
Sample Name	SRPK2_BGKLV34-39	SRPK2_BGKLV34-40
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	89,121,404	80,685,636
total_aligned_reads	73,422,966	67,344,166
unique_aligned_reads	66,864,116	61,288,510
percent_uniqueAligned	0.75026	0.75960
correlation_replicates	0.999599	0.999599
spikein_reads	370,268	332,332
percent_spikeins	0.00415	0.00412
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1575	1576

Data Submission Information

	BGKLV34-39	BGKLV34-39
ENCODE_alias	brenton-graveley:SRPK2_BGKLV34	brenton-graveley:SRPK2-BGKLV34-K562
ENCODE_accession	ENCSR524YXQ	ENCSR231HOJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-39	BGKLV34-39
Sample Name	SRPK2_BGKLV34-39	SRPK2_BGKLV34-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3160	6965

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_BGKLV34-39_GATCAG_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1575	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21534
SRPK2_BGKLV34-39_GATCAG_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1575	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21554
SRPK2_BGKLV34-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1575					GRCh38	V40	SRPK2_BGKLV34-39_GATCAG_L004_001.R1.fastq.gz,SRPK2_BGKLV34-39_GATCAG_L004_001.R2.fastq.gz		ENCORE2	21574
SRPK2_BGKLV34-39_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1575					GRCh38	V40	SRPK2_BGKLV34-39/Aligned.sortedByCoord.out.bam		ENCORE2	21594
SRPK2_BGKLV34-39_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1575					GRCh38	V40	SRPK2_BGKLV34-39/Aligned.sortedByCoord.out.bam		ENCORE2	21614
SRPK2_BGKLV34-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1575					GRCh38	V40	SRPK2_BGKLV34-39/Aligned.sortedByCoord.out.bam		ENCORE2	21634
SRPK2_BGKLV34-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1575					GRCh38	V40	SRPK2_BGKLV34-39/Aligned.sortedByCoord.out.bam		ENCORE2	21654
SRPK2_BGKLV34-39_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1575					GRCh38	V40	SRPK2_BGKLV34-39_GATCAG_L004_001.R1.fastq.gz,SRPK2_BGKLV34-39_GATCAG_L004_001.R2.fastq.gz		ENCORE2	21674
SRPK2_BGKLV34-40_TAGCTT_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1576	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21535
SRPK2_BGKLV34-40_TAGCTT_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1576	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21555
SRPK2_BGKLV34-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1576					GRCh38	V40	SRPK2_BGKLV34-40_TAGCTT_L004_001.R1.fastq.gz,SRPK2_BGKLV34-40_TAGCTT_L004_001.R2.fastq.gz		ENCORE2	21575
SRPK2_BGKLV34-40_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1576					GRCh38	V40	SRPK2_BGKLV34-40/Aligned.sortedByCoord.out.bam		ENCORE2	21595
SRPK2_BGKLV34-40_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1576					GRCh38	V40	SRPK2_BGKLV34-40/Aligned.sortedByCoord.out.bam		ENCORE2	21615
SRPK2_BGKLV34-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1576					GRCh38	V40	SRPK2_BGKLV34-40/Aligned.sortedByCoord.out.bam		ENCORE2	21635
SRPK2_BGKLV34-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1576					GRCh38	V40	SRPK2_BGKLV34-40/Aligned.sortedByCoord.out.bam		ENCORE2	21655
SRPK2_BGKLV34-40_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1576					GRCh38	V40	SRPK2_BGKLV34-40_TAGCTT_L004_001.R1.fastq.gz,SRPK2_BGKLV34-40_TAGCTT_L004_001.R2.fastq.gz		ENCORE2	21675