SRSF9 RNA-Seq in K562

General Information


RBP	SRSF9
Cell_Line	K562
Method	CRISPR
Exp_Name	SRSF9-BGKcLV06-K562
ENCODE_series_ID	ENCSR420GEF
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR972AZD
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	SRSF9-BGKcLV06-35
Rep2	SRSF9-BGKcLV06-36
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	85.9
Rep2_qPCR	88.8
Rep1_WB	85.9
Rep2_WB	78.4
Antibody Cat#	RN081PW
Antibody Lot#
Antibody DCC ID	ENCAB278ULX
Status	Released
Project	ENCODE3
ID	778

Experiment Information (Status: Released)

	BGKcLV06-35	BGKcLV06-36
idx	211	212
TRCN#_or_BGC#	BGC#0000072	BGC#0000072
shRNA_or_gRNA_sequence	ATCGAGCTCAAGAACCGGCA	ATCGAGCTCAAGAACCGGCA
PAM
Name	SRSF9_91F	SRSF9_91F
Sample_ID	BGKcLV06-35	BGKcLV06-36
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	SRSF9	SRSF9
qPCR_result	85.9	88.8
Ave_qPCR	87.4
RT-qPCR_primer-F	ATATGCCCTGCGTAAACTGG
RT-qPCR_primer-R	AGCTGGTGCTTCTCTCAGGA
protein_conc	2038	2037
WB_result	85.9	78.4
Ave_WB	82.1
WB_DONE_date	6/23/17
MW	26kD
IP
antibody_Cat#	RN081PW
Antibody DCC ID	ENCAB278ULX	ENCAB278ULX
submitted_to_DCC_date	9/29/17
Rep1_TPM	137.1	0
Rep2_TPM	121.9	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4309	4310

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF9	Product_ID: RN081PW Lot_ID: 1 Source: MBLI Target Name: SRSF9-human

Experiment Status

	BGKcLV06-35	BGKcLV06-36
Sample_ID	BGKcLV06-35	BGKcLV06-36
Sample Name	SRSF9-BGKcLV06-35	SRSF9-BGKcLV06-36
Sample Name	SRSF9-BGKcLV06-35	SRSF9-BGKcLV06-36
RBP	SRSF9	SRSF9
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1373	1374

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-35	BGKcLV06-36
Sample #
Sample Name	SRSF9-BGKcLV06-35	SRSF9-BGKcLV06-36
Sample_Name_Alias	SRSF9-BGKcLV06-35	SRSF9-BGKcLV06-36
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/G2.png	DNA_Library_set39/set2/H2.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set39/set3/D2.png	RNA_Library_set39/set3/E2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-35	BGKcLV06-36
RBP	SRSF9	SRSF9
Batch_ID	BGKcLV06	BGKcLV06
WB_result	85.900	78.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3068	3069

Sequencing Information

	BGKcLV06-35	BGKcLV06-36
Sample_ID	BGKcLV06-35	BGKcLV06-36
Sample Name	SRSF9-BGKcLV06-35	SRSF9-BGKcLV06-36
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	79,575,096	58,539,586
total_aligned_reads	72,065,812	52,686,986
unique_aligned_reads	65,226,844	47,875,686
percent_uniqueAligned	0.81969	0.81783
correlation_replicates	0.994232	0.994232
spikein_reads	34,982	31,544
percent_spikeins	0.00044	0.00054
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1719	1720

Data Submission Information

	BGKcLV06-35	BGKcLV06-35
ENCODE_alias	brenton-graveley:SRSF9-BGKcLV06	brenton-graveley:SRSF9-BGKcLV06-K562
ENCODE_accession	ENCSR972AZD	ENCSR420GEF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-35	BGKcLV06-35
Sample Name	SRSF9-BGKcLV06-35	SRSF9-BGKcLV06-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3226	6979

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
SRSF9-BGKcLV06-35_ACTGAT_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1719	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22488
SRSF9-BGKcLV06-35_ACTGAT_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1719	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22524
SRSF9-BGKcLV06-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1719					GRCh38	V40	SRSF9-BGKcLV06-35_ACTGAT_ACBE67ANXX_L006_001.R1.fastq.gz,SRSF9-BGKcLV06-35_ACTGAT_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22560
SRSF9-BGKcLV06-35_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1719					GRCh38	V40	SRSF9-BGKcLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	22596
SRSF9-BGKcLV06-35_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1719					GRCh38	V40	SRSF9-BGKcLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	22632
SRSF9-BGKcLV06-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1719					GRCh38	V40	SRSF9-BGKcLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	22668
SRSF9-BGKcLV06-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1719					GRCh38	V40	SRSF9-BGKcLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	22704
SRSF9-BGKcLV06-35_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1719					GRCh38	V40	SRSF9-BGKcLV06-35_ACTGAT_ACBE67ANXX_L006_001.R1.fastq.gz,SRSF9-BGKcLV06-35_ACTGAT_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22740
SRSF9-BGKcLV06-36_ATTCCT_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1720	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22489
SRSF9-BGKcLV06-36_ATTCCT_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1720	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22525
SRSF9-BGKcLV06-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1720					GRCh38	V40	SRSF9-BGKcLV06-36_ATTCCT_ACBE67ANXX_L006_001.R1.fastq.gz,SRSF9-BGKcLV06-36_ATTCCT_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22561
SRSF9-BGKcLV06-36_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1720					GRCh38	V40	SRSF9-BGKcLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	22597
SRSF9-BGKcLV06-36_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1720					GRCh38	V40	SRSF9-BGKcLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	22633
SRSF9-BGKcLV06-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1720					GRCh38	V40	SRSF9-BGKcLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	22669
SRSF9-BGKcLV06-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1720					GRCh38	V40	SRSF9-BGKcLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	22705
SRSF9-BGKcLV06-36_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1720					GRCh38	V40	SRSF9-BGKcLV06-36_ATTCCT_ACBE67ANXX_L006_001.R1.fastq.gz,SRSF9-BGKcLV06-36_ATTCCT_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22741