SRSF5 RNA-Seq in K562

General Information


RBP	SRSF5
Cell_Line	K562
Method	CRISPR
Exp_Name	SRSF5-BGKcLV11-K562
ENCODE_series_ID	ENCSR303KSC
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR528YVC
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	SRSF5-BGKcLV11-95
Rep2	SRSF5-BGKcLV11-96
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	49.7
Rep2_qPCR	45.1
Rep1_WB	92.2
Rep2_WB	96.4
Antibody Cat#	RN082PW
Antibody Lot#
Antibody DCC ID	ENCAB038XFS
Status	Released
Project	ENCODE4
ID	192

Experiment Information (Status: Released)

	BGKcLV11-95	BGKcLV11-96
idx	411	412
TRCN#_or_BGC#	BGC#0000212	BGC#0000212
shRNA_or_gRNA_sequence	GAGGTCTGCGACTACTAAAA	GAGGTCTGCGACTACTAAAA
PAM	CGG	CGG
Name	SRSF5_92F	SRSF5_92F
Sample_ID	BGKcLV11-95	BGKcLV11-96
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	SRSF5	SRSF5
qPCR_result	49.7	45.1
Ave_qPCR	47.4
RT-qPCR_primer-F	TCAAGGGATATGGACGGATAA
RT-qPCR_primer-R	CCATCAAGCTCATACACAGCA
protein_conc	3431	3209
WB_result	92.2	96.4
Ave_WB	94.3
WB_DONE_date	1/30/19
MW	31 kDa
IP
antibody_Cat#	RN082PW
Antibody DCC ID	ENCAB038XFS
submitted_to_DCC_date	2/22/19
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4513	4514

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF5	Product_ID: RN082PW Lot_ID: 1 Source: MBLI Target Name: SRSF5-human

Experiment Status

	BGKcLV11-95	BGKcLV11-96
Sample_ID	BGKcLV11-95	BGKcLV11-96
Sample Name	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-96
Sample Name	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-96
RBP	SRSF5	SRSF5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2693	2694

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-95	BGKcLV11-96
Sample #	21	22
Sample Name	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-96
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	2-E1	2-F1
Tecan	47.89	48.76
Tecan_date	2019-03-13	2019-03-13
Size_bp	292	298
Peak_Molarity	158.00	144.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/E3.png	DNA_Library_set42/set1/F3.png
RIN	8.4	7.8
libSample_RNA_Well	RNA_Library_set42/set1/E3.png	RNA_Library_set42/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-95	BGKcLV11-96
RBP	SRSF5	SRSF5
Batch_ID	BGKcLV11	BGKcLV11
WB_result	92.200	96.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	21	22

Sequencing Information

	BGKcLV11-95	BGKcLV11-96
Sample_ID	BGKcLV11-95	BGKcLV11-96
Sample Name	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-96
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	107,911,696	38,728,630
total_aligned_reads	103,960,038	37,994,994
unique_aligned_reads	93,580,670	34,336,132
percent_uniqueAligned	0.86720	0.88658
correlation_replicates	0.995471	0.995471
spikein_reads	170,092	63,392
percent_spikeins	0.00158	0.00164
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	71	72

Data Submission Information

	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-96	BGKcLV11-96	BGKcLV11-96	BGKcLV11-96
ENCODE_alias	brenton-graveley:SRSF5-BGKcLV11	brenton-graveley:SRSF5-BGKcLV11-95	brenton-graveley:L-SRSF5-BGKcLV11-95	brenton-graveley:SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF5-BGKcLV11-K562	brenton-graveley:SRSF5-BGKcLV11-96	brenton-graveley:L-SRSF5-BGKcLV11-96	brenton-graveley:SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR528YVC	ENCBS778ZTA	ENCLB396RFQ	ENCFF634BAP	ENCFF240HLE	ENCSR303KSC	ENCBS486UHL	ENCLB171MSR	ENCFF465SGD	ENCFF113CEW
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	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-95	BGKcLV11-96	BGKcLV11-96	BGKcLV11-96	BGKcLV11-96
Sample Name	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-95	SRSF5-BGKcLV11-96	SRSF5-BGKcLV11-96	SRSF5-BGKcLV11-96	SRSF5-BGKcLV11-96
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		SRSF5-BGKcLV11-95.pdf	L-SRSF5-BGKcLV11-95.pdf				SRSF5-BGKcLV11-96.pdf	L-SRSF5-BGKcLV11-96.pdf
ID	771	837	919	1021	1103	7337	838	920	1022	1104

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
SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	71	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	403
SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	71	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	485
SRSF5-BGKcLV11-95_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	71					GRCh38	V40	SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23742
SRSF5-BGKcLV11-95_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	71					GRCh38	V40	SRSF5-BGKcLV11-95/Aligned.sortedByCoord.out.bam		ENCORE2	23824
SRSF5-BGKcLV11-95_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	71					GRCh38	V40	SRSF5-BGKcLV11-95/Aligned.sortedByCoord.out.bam		ENCORE2	23906
SRSF5-BGKcLV11-95_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	71					GRCh38	V40	SRSF5-BGKcLV11-95/Aligned.sortedByCoord.out.bam		ENCORE2	23988
SRSF5-BGKcLV11-95_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	71					GRCh38	V40	SRSF5-BGKcLV11-95/Aligned.sortedByCoord.out.bam		ENCORE2	24070
SRSF5-BGKcLV11-95_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	71					GRCh38	V40	SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRSF5-BGKcLV11-95_GGTACCTT+AAGACGTC_HK3H2DSXX_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24152
SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	72	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	404
SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	72	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	486
SRSF5-BGKcLV11-96_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	72					GRCh38	V40	SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23743
SRSF5-BGKcLV11-96_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	72					GRCh38	V40	SRSF5-BGKcLV11-96/Aligned.sortedByCoord.out.bam		ENCORE2	23825
SRSF5-BGKcLV11-96_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	72					GRCh38	V40	SRSF5-BGKcLV11-96/Aligned.sortedByCoord.out.bam		ENCORE2	23907
SRSF5-BGKcLV11-96_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	72					GRCh38	V40	SRSF5-BGKcLV11-96/Aligned.sortedByCoord.out.bam		ENCORE2	23989
SRSF5-BGKcLV11-96_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	72					GRCh38	V40	SRSF5-BGKcLV11-96/Aligned.sortedByCoord.out.bam		ENCORE2	24071
SRSF5-BGKcLV11-96_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	72					GRCh38	V40	SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz,SRSF5-BGKcLV11-96_AACGTTCC+GGAGTACT_HK3H2DSXX_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24153