SRSF9 RNA-Seq in HepG2

General Information


RBP	SRSF9
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRSF9-BGHcLV09-HepG2
ENCODE_series_ID	ENCSR469IED
Batch_ID	BGHcLV09
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR814JQP
ENCODE_CN_Exp_ID	ENCSR300EBW
Rep1	SRSF9-BGHcLV09-21
Rep2	SRSF9-BGHcLV09-22
CN1	NT-BGHcLV09-1
CN2	NT-BGHcLV09-2
Rep1_qPCR	86.0
Rep2_qPCR	88.4
Rep1_WB	64.2
Rep2_WB	51.0
Antibody Cat#	RN081PW
Antibody Lot#
Antibody DCC ID	ENCAB278ULX
Status	Released
Project	ENCODE4
ID	219

Experiment Information (Status: Released)

	BGHcLV09-21	BGHcLV09-22
idx	183	184
TRCN#_or_BGC#	BGC#0000151	BGC#0000151
shRNA_or_gRNA_sequence	GGGGTCCTCGAAGCGCACGA	GGGGTCCTCGAAGCGCACGA
PAM	AGG	AGG
Name	SRSF9-86F	SRSF9-86F
Sample_ID	BGHcLV09-21	BGHcLV09-22
transduction_Date	4/20/18	4/20/18
days	D6	D6
RBP_name	SRSF9	SRSF9
qPCR_result	86.0	88.4
Ave_qPCR	87.2
RT-qPCR_primer-F	ATATGCCCTGCGTAAACTGG
RT-qPCR_primer-R	AGCTGGTGCTTCTCTCAGGA
protein_conc	4187	3142
WB_result	64.2	51.0
Ave_WB	57.6
WB_DONE_date	4/30/18
MW	26kD
IP
antibody_Cat#	RN081PW
Antibody DCC ID	ENCAB278ULX
submitted_to_DCC_date	9/6/18
Rep1_TPM	154	0
Rep2_TPM	142	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6326	6327

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

	BGHcLV09-21	BGHcLV09-22
Sample_ID	BGHcLV09-21	BGHcLV09-22
Sample Name
Sample Name	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-22
RBP	SRSF9	SRSF9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6265	6266

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV09-21	BGHcLV09-22
Sample #	47	48
Sample Name	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-22
Sample_Name_Alias
Index Well Position	C07	D07
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	265	275
Peak_Molarity	39.90	34.10
libSampleQC_DNA_Well	DNA_Library_set41/set5/C7.png	DNA_Library_set41/set5/D7.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set41/set1/G6.png	RNA_Library_set41/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV09-21	BGHcLV09-22
RBP	SRSF9	SRSF9
Batch_ID	BGHcLV09	BGHcLV09
WB_result	64.200	51.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	897	898

Sequencing Information

	BGHcLV09-21	BGHcLV09-22
Sample_ID	BGHcLV09-21	BGHcLV09-22
Sample Name	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-22
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	108,930,000	132,656,858
total_aligned_reads	107,186,802	130,986,018
unique_aligned_reads	98,752,226	121,142,012
percent_uniqueAligned	0.90657	0.91320
correlation_replicates	0.994999	0.994999
spikein_reads	113,842	136,882
percent_spikeins	0.00105	0.00103
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	303	304

Data Submission Information

	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-22	BGHcLV09-22	BGHcLV09-22	BGHcLV09-22
ENCODE_alias	brenton-graveley:SRSF9-BGHcLV09	brenton-graveley:SRSF9-BGHcLV09-21	brenton-graveley:L-SRSF9-BGHcLV09-21	brenton-graveley:SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF9-BGHcLV09-HepG2	brenton-graveley:SRSF9-BGHcLV09-22	brenton-graveley:L-SRSF9-BGHcLV09-22	brenton-graveley:SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR814JQP	ENCBS986HKN	ENCLB302UCC	ENCFF558DPZ	ENCFF169FEG	ENCSR469IED	ENCBS151QTT	ENCLB054VXK	ENCFF636MSL	ENCFF201RGO
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	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-21	BGHcLV09-22	BGHcLV09-22	BGHcLV09-22	BGHcLV09-22
Sample Name	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-21	SRSF9-BGHcLV09-22	SRSF9-BGHcLV09-22	SRSF9-BGHcLV09-22	SRSF9-BGHcLV09-22
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		SRSF9-BGHcLV09-21.pdf	L-SRSF9-BGHcLV09-21.pdf				SRSF9-BGHcLV09-22.pdf	L-SRSF9-BGHcLV09-22.pdf
ID	1143	1206	1276	1346	1410	7338	1207	1277	1347	1411

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
SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	303				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	553
SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	303				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	623
SRSF9-BGHcLV09-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	303	GRCh38	V40	SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26791
SRSF9-BGHcLV09-21_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	303	GRCh38	V40	SRSF9-BGHcLV09-21/Aligned.sortedByCoord.out.bam		ENCORE2	26861
SRSF9-BGHcLV09-21_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	303	GRCh38	V40	SRSF9-BGHcLV09-21/Aligned.sortedByCoord.out.bam		ENCORE2	26931
SRSF9-BGHcLV09-21_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	303	GRCh38	V40	SRSF9-BGHcLV09-21/Aligned.sortedByCoord.out.bam		ENCORE2	27001
SRSF9-BGHcLV09-21_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	303	GRCh38	V40	SRSF9-BGHcLV09-21/Aligned.sortedByCoord.out.bam		ENCORE2	27071
SRSF9-BGHcLV09-21_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	303	GRCh38	V40	SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF9-BGHcLV09-21_AACAGGTT+ATACCAAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27141
SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	304				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	554
SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	304				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	624
SRSF9-BGHcLV09-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	304	GRCh38	V40	SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26792
SRSF9-BGHcLV09-22_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	304	GRCh38	V40	SRSF9-BGHcLV09-22/Aligned.sortedByCoord.out.bam		ENCORE2	26862
SRSF9-BGHcLV09-22_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	304	GRCh38	V40	SRSF9-BGHcLV09-22/Aligned.sortedByCoord.out.bam		ENCORE2	26932
SRSF9-BGHcLV09-22_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	304	GRCh38	V40	SRSF9-BGHcLV09-22/Aligned.sortedByCoord.out.bam		ENCORE2	27002
SRSF9-BGHcLV09-22_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	304	GRCh38	V40	SRSF9-BGHcLV09-22/Aligned.sortedByCoord.out.bam		ENCORE2	27072
SRSF9-BGHcLV09-22_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	304	GRCh38	V40	SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRSF9-BGHcLV09-22_GGTGAACC+GCGTTGGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27142