SRPK1 RNA-Seq in K562

General Information


RBP	SRPK1
Cell_Line	K562
Method	CRISPR
Exp_Name	SRPK1-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	SRPK1-BGKcLV37-39
Rep2	SRPK1-BGKcLV37-40
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	51.1
Rep2_qPCR	41.3
Rep1_WB	66.0
Rep2_WB	57.0
Antibody Cat#	A302-461A
Antibody Lot#	lot # 1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1058

Experiment Information (Status: Submitting)

	BGKcLV37-39	BGKcLV37-39	BGKcLV37-40	BGKcLV37-40
idx	1391	0	1392	0
TRCN#_or_BGC#	BGC#0001055	BGC#0001055	BGC#0001055	BGC#0001055
shRNA_or_gRNA_sequence	AGCCTAACTTTCGGATCACA	AGCCTAACTTTCGGATCACA	AGCCTAACTTTCGGATCACA	AGCCTAACTTTCGGATCACA
PAM	TGG	TGG	TGG	TGG
Name	SRPK1_91	SRPK1_91	SRPK1_91	SRPK1_91
Sample_ID	BGKcLV37-39	BGKcLV37-39	BGKcLV37-40	BGKcLV37-40
transduction_Date	9/20/22	9/20/22	9/20/22	9/20/22
days	D6	D6	D6	D6
RBP_name	SRPK1	SRPK1	SRPK1	SRPK1
qPCR_result	51.1	51.1	41.3	41.3
Ave_qPCR	46.2	46.2
RT-qPCR_primer-F	gggcagagataccctgtgaa	gggcagagataccctgtgaa
RT-qPCR_primer-R	tggctcaaggggattaacaa	tggctcaaggggattaacaa
protein_conc	1633	1633	1448	1448
WB_result	66.0	95.6	57.0	95.2
Ave_WB	61.5	95.4
WB_DONE_date	9/29/22,10/12/23	8/2/23	Licor
MW	74kd	74kd
IP
antibody_Cat#	A302-461A	A302-462A	lot # 1	lot # 1
Antibody DCC ID	NO ID	NO ID
submitted_to_DCC_date	8/29/23	8/29/23
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5543	5545	5544	5546

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRPK1	Product_ID: A302-461A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPK1-human
SRPK1	Product_ID: A302-462A Lot_ID: 1 Source: Bethyl Labs Target Name: SRPK1-human

Experiment Status

	BGKcLV37-39	BGKcLV37-40
Sample_ID	BGKcLV37-39	BGKcLV37-40
Sample Name
Sample Name	SRPK1-BGKcLV37-39	SRPK1-BGKcLV37-40
RBP	SRPK1	SRPK1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11100	11101

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-39	BGKcLV37-40
Sample #	39	40
Sample Name	SRPK1-BGKcLV37-39	SRPK1-BGKcLV37-40
Sample_Name_Alias
Index Well Position	G05	H05
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	297
Peak_Molarity	55.10	42.40
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/G5.png	DNA_Library_set54-56/set1/H5.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/G5.png	RNA_Library_set54-56/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-39	BGKcLV37-40
RBP	SRPK1	SRPK1
Batch_ID	BGKcLV37	BGKcLV37
WB_result	54.600	51.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3410	3411

Sequencing Information

	BGKcLV37-39	BGKcLV37-40
Sample_ID	BGKcLV37-39	BGKcLV37-40
Sample Name	SRPK1-BGKcLV37-39	SRPK1-BGKcLV37-40
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	44,760,084	39,831,175
total_aligned_reads	42,805,974	37,788,929
unique_aligned_reads	39,660,465	35,138,430
percent_uniqueAligned	0.88607	0.88218
correlation_replicates	0.980972	0.980972
spikein_reads	4,124	6,192
percent_spikeins	0.00009	0.00016
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2283	2284

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-BGKcLV37-39_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2283	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	8408
SRPK1-BGKcLV37-39_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2283	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	8458
SRPK1-BGKcLV37-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2283					GRCh38	V40	SRPK1-BGKcLV37-39_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGKcLV37-39_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25649
SRPK1-BGKcLV37-39_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	2283					GRCh38	V40	SRPK1-BGKcLV37-39/Aligned.sortedByCoord.out.bam		ENCORE2	25699
SRPK1-BGKcLV37-39_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	2283					GRCh38	V40	SRPK1-BGKcLV37-39/Aligned.sortedByCoord.out.bam		ENCORE2	25749
SRPK1-BGKcLV37-39_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	2283					GRCh38	V40	SRPK1-BGKcLV37-39/Aligned.sortedByCoord.out.bam		ENCORE2	25799
SRPK1-BGKcLV37-39_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	2283					GRCh38	V40	SRPK1-BGKcLV37-39/Aligned.sortedByCoord.out.bam		ENCORE2	25849
SRPK1-BGKcLV37-39_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2283					GRCh38	V40	SRPK1-BGKcLV37-39_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGKcLV37-39_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25899
SRPK1-BGKcLV37-40_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2284	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	8409
SRPK1-BGKcLV37-40_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2284	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	8459
SRPK1-BGKcLV37-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2284					GRCh38	V40	SRPK1-BGKcLV37-40_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGKcLV37-40_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25650
SRPK1-BGKcLV37-40_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	2284					GRCh38	V40	SRPK1-BGKcLV37-40/Aligned.sortedByCoord.out.bam		ENCORE2	25700
SRPK1-BGKcLV37-40_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	2284					GRCh38	V40	SRPK1-BGKcLV37-40/Aligned.sortedByCoord.out.bam		ENCORE2	25750
SRPK1-BGKcLV37-40_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	2284					GRCh38	V40	SRPK1-BGKcLV37-40/Aligned.sortedByCoord.out.bam		ENCORE2	25800
SRPK1-BGKcLV37-40_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	2284					GRCh38	V40	SRPK1-BGKcLV37-40/Aligned.sortedByCoord.out.bam		ENCORE2	25850
SRPK1-BGKcLV37-40_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2284					GRCh38	V40	SRPK1-BGKcLV37-40_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPK1-BGKcLV37-40_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25900