SRSF3 RNA-Seq in K562

General Information


RBP	SRSF3
Cell_Line	K562
Method	CRISPR
Exp_Name	SRSF3-BGKcLV08-K562
ENCODE_series_ID	ENCSR568CDK
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR914IEV
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	SRSF3-BGKcLV08-75
Rep2	SRSF3-BGKcLV08-76
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	75.3
Rep2_WB	80.6
Antibody Cat#	PN080PW
Antibody Lot#	PN080PW
Antibody DCC ID	ENCAB701PQV
Status	Released
Project	ENCODE4
ID	211

Experiment Information (Status: Released)

	BGKcLV08-75	BGKcLV08-76
idx	300	301
TRCN#_or_BGC#	BGC#0000149	BGC#0000149
shRNA_or_gRNA_sequence	CTCGAGATGATTATCGTAGG	CTCGAGATGATTATCGTAGG
PAM	AGG	AGG
Name	SRSF3-87F	SRSF3-87F
Sample_ID	BGKcLV08-75	BGKcLV08-76
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	SRSF3	SRSF3
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ATGCAGCTGATGCAGTCC
RT-qPCR_primer-R	TTCACCATTCGACAGTTCCA
protein_conc	2602	2494
WB_result	75.3	80.6
Ave_WB	77.9
WB_DONE_date	3/27/18
MW	20kDa
IP
antibody_Cat#	PN080PW	PN080PW
Antibody DCC ID	ENCAB701PQV
submitted_to_DCC_date	9/6/18
Rep1_TPM	177.5	0
Rep2_TPM	158.2	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4400	4401

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF3	Product_ID: RN080PW Lot_ID: 1 Source: MBLI Target Name: SRSF3-human

Experiment Status

	BGKcLV08-75	BGKcLV08-76
Sample_ID	BGKcLV08-75	BGKcLV08-76
Sample Name
Sample Name	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-76
RBP	SRSF3	SRSF3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6193	6194

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-75	BGKcLV08-76
Sample #	29	30
Sample Name	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-76
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	278	278
Peak_Molarity	60.10	67.80
libSampleQC_DNA_Well	DNA_Library_set41/set2/E4.png	DNA_Library_set41/set2/F4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set41/set1/E4.png	RNA_Library_set41/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-75	BGKcLV08-76
RBP	SRSF3	SRSF3
Batch_ID	BGKcLV08	BGKcLV08
WB_result	75.300	80.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	879	880

Sequencing Information

	BGKcLV08-75	BGKcLV08-76
Sample_ID	BGKcLV08-75	BGKcLV08-76
Sample Name	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-76
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	190,615,316	271,949,128
total_aligned_reads	186,525,990	262,746,256
unique_aligned_reads	167,769,620	236,827,282
percent_uniqueAligned	0.88015	0.87085
correlation_replicates	0.997044	0.997044
spikein_reads	295,752	453,328
percent_spikeins	0.00155	0.00167
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	285	286

Data Submission Information

	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-76	BGKcLV08-76	BGKcLV08-76	BGKcLV08-76
ENCODE_alias	brenton-graveley:SRSF3-BGKcLV08	brenton-graveley:SRSF3-BGKcLV08-75	brenton-graveley:L-SRSF3-BGKcLV08-75	brenton-graveley:SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF3-BGKcLV08-K562	brenton-graveley:SRSF3-BGKcLV08-76	brenton-graveley:L-SRSF3-BGKcLV08-76	brenton-graveley:SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR914IEV	ENCBS978SXT	ENCLB795YCM	ENCFF894NFP	ENCFF065TWD	ENCSR568CDK	ENCBS251FSC	ENCLB391DMF	ENCFF595NNR	ENCFF983XMH
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	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-75	BGKcLV08-76	BGKcLV08-76	BGKcLV08-76	BGKcLV08-76
Sample Name	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-75	SRSF3-BGKcLV08-76	SRSF3-BGKcLV08-76	SRSF3-BGKcLV08-76	SRSF3-BGKcLV08-76
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
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		SRSF3-BGKcLV08-75.pdf	L-SRSF3-BGKcLV08-75.pdf				SRSF3-BGKcLV08-76.pdf	L-SRSF3-BGKcLV08-76.pdf
ID	1142	1204	1274	1344	1408	7336	1205	1275	1345	1409

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	285				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	551
SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	285				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	621
SRSF3-BGKcLV08-75_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	285	GRCh38	V40	SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26789
SRSF3-BGKcLV08-75_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	285	GRCh38	V40	SRSF3-BGKcLV08-75/Aligned.sortedByCoord.out.bam		ENCORE2	26859
SRSF3-BGKcLV08-75_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	285	GRCh38	V40	SRSF3-BGKcLV08-75/Aligned.sortedByCoord.out.bam		ENCORE2	26929
SRSF3-BGKcLV08-75_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	285	GRCh38	V40	SRSF3-BGKcLV08-75/Aligned.sortedByCoord.out.bam		ENCORE2	26999
SRSF3-BGKcLV08-75_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	285	GRCh38	V40	SRSF3-BGKcLV08-75/Aligned.sortedByCoord.out.bam		ENCORE2	27069
SRSF3-BGKcLV08-75_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	285	GRCh38	V40	SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF3-BGKcLV08-75_CCGTGAAG+CAGTGGAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27139
SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	286				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	552
SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	286				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	622
SRSF3-BGKcLV08-76_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	286	GRCh38	V40	SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26790
SRSF3-BGKcLV08-76_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	286	GRCh38	V40	SRSF3-BGKcLV08-76/Aligned.sortedByCoord.out.bam		ENCORE2	26860
SRSF3-BGKcLV08-76_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	286	GRCh38	V40	SRSF3-BGKcLV08-76/Aligned.sortedByCoord.out.bam		ENCORE2	26930
SRSF3-BGKcLV08-76_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	286	GRCh38	V40	SRSF3-BGKcLV08-76/Aligned.sortedByCoord.out.bam		ENCORE2	27000
SRSF3-BGKcLV08-76_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	286	GRCh38	V40	SRSF3-BGKcLV08-76/Aligned.sortedByCoord.out.bam		ENCORE2	27070
SRSF3-BGKcLV08-76_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	286	GRCh38	V40	SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF3-BGKcLV08-76_TTACAGGA+TGACAAGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27140