SRSF4 RNA-Seq in HepG2

General Information


RBP	SRSF4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRSF4-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR106USG
Batch_ID	BGHcLV05
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR929JKA
ENCODE_CN_Exp_ID	ENCSR805TIZ
Rep1	SRSF4-BGHcLV05-33D
Rep2	SRSF4-BGHcLV05-34D
CN1	NT-BGHcLV05-1D
CN2	NT-BGHcLV05-2D
Rep1_qPCR	24.28850809
Rep2_qPCR	11.3510537
Rep1_WB	54.8
Rep2_WB	57.2
Antibody Cat#	A303-670A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB653SNR
Status	Released
Project	ENCODE4
ID	889

Experiment Information (Status: Released)

	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
idx	69	108	70	109
TRCN#_or_BGC#	BGC#0000054	BGC#0000054	BGC#0000054	BGC#0000054
shRNA_or_gRNA_sequence	CCGTAACTGCCATCTCGCCG	CCGTAACTGCCATCTCGCCG	CCGTAACTGCCATCTCGCCG	CCGTAACTGCCATCTCGCCG
PAM
Name	SRSF4_1	SRSF4_1	SRSF4_1	SRSF4_1
Sample_ID	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	SRSF4	SRSF4	SRSF4	SRSF4
qPCR_result	24.3		11.4
Ave_qPCR	17.8
RT-qPCR_primer-F	AATATGGCCCTCCTACTCGC
RT-qPCR_primer-R	TCTCCTGCCTGACGCATATAAT
protein_conc	3493	0	3712	0
WB_result	54.8		57.2
Ave_WB	56.0
WB_DONE_date	3/28/17
MW	56 kDa
IP	1MW
antibody_Cat#	A303-670A		A303-670A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	52	63	0	0
Rep2_TPM	56	73	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library	5/11/17		5/11/17
Note
ID	8260	8297	8261	8298

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
Sample_ID	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
Sample Name	SRSF4-BGHcLV05-33B		SRSF4-BGHcLV05-34B
Sample Name	SRSF4-BGHcLV05-33B	SRSF4-BGHcLV05-33D	SRSF4-BGHcLV05-34B	SRSF4-BGHcLV05-34D
RBP	SRSF4	SRSF4	SRSF4	SRSF4
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	Released	Released	Released
Status_date	2017-11-20	2022-03-07	2017-11-20	2022-03-07
Project	ENCODE3	ENCODE4	ENCODE3	ENCODE4
Note
ID	1357	10463	1358	10464

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
Sample #		83		84
Sample Name	SRSF4-BGHcLV05-33B	SRSF4-BGHcLV05-33D	SRSF4-BGHcLV05-34B	SRSF4-BGHcLV05-34D
Sample_Name_Alias	SRSF4-BGHcLV05-33B		SRSF4-BGHcLV05-34B
Index Well Position	S03	S03	S04	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-05-11	2018-11-19	2017-05-11	2018-11-19
Lib_ID	Lib-170511	Lib-181119	Lib-170511	Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp		284		287
Peak_Molarity		81.10		74.10
libSampleQC_DNA_Well	DNA_Library_set39/set2/C8.png	DNA_Library_set41/set1/C10.png	DNA_Library_set39/set2/D8.png	DNA_Library_set41/set1/D10.png
RIN	9.6	9.6	9.6	9.6
libSample_RNA_Well	RNA_Library_set39/set4/E1.png	RNA_Library_set39/set4/E1.png	RNA_Library_set39/set4/F1.png	RNA_Library_set39/set4/F1.png
SampleQC_method		TapeStation		TapeStation
SampleQC_date		2022-03-01		2022-03-01
Sample_ID	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
RBP	SRSF4	SRSF4	SRSF4	SRSF4
Batch_ID	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05
WB_result	54.800	54.800	57.200	57.200
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	D	B	D
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE4	ENCODE3	ENCODE4
ID	3052	3260	3053	3261

Sequencing Information

	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
Sample_ID	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
Sample Name	SRSF4-BGHcLV05-33B	SRSF4-BGHcLV05-33D	SRSF4-BGHcLV05-34B	SRSF4-BGHcLV05-34D
Pool ID	Pool-170911	Pool-181119	Pool-170911	Pool-181119
LocalServer_folder	set39_H	set41_spikeins	set39_H	set41_spikeins
total_reads	84,993,172	126,413,214	42,099,994	140,999,198
total_aligned_reads	74,682,752	97,322,474	37,328,324	113,701,736
unique_aligned_reads	70,295,868	91,477,048	35,224,442	106,950,278
percent_uniqueAligned	0.82708	0.72364	0.83669	0.75852
correlation_replicates	0.987696	0.993427	0.987696	0.993427
spikein_reads	14	144,968	2	155,586
percent_spikeins		0.00115		0.00110
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1703	1973	1704	1974

Data Submission Information

	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
ENCODE_alias	brenton-graveley:SRSF4-BGHcLV05-B	brenton-graveley:SRSF4-BGHcLV05-HepG2_A	brenton-graveley:SRSF4-BGHcLV05-D	brenton-graveley:L-SRSF4-BGHcLV05-33D	brenton-graveley:SRSF4-BGHcLV05-HepG2	brenton-graveley:SRSF4-BGHcLV05-33B	brenton-graveley:L-SRSF4-BGHcLV05-34D	brenton-graveley:SRSF4-BGHcLV05-34B
ENCODE_accession	ENCSR471INA	ENCSR578UEB	ENCSR929JKA	ENCLB918RSA	ENCSR106USG	ENCBS284JIL	ENCLB314ELS	ENCBS775SLR
object_type	experiment	experiment	experiment	library	gene_silencing_series	biosample	library	biosample
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
Sample_ID	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-33	BGHcLV05-34	BGHcLV05-34
Sample Name	SRSF4-BGHcLV05-33B	SRSF4-BGHcLV05-33B	SRSF4-BGHcLV05-33D	SRSF4-BGHcLV05-33D	SRSF4-BGHcLV05-33D	SRSF4-BGHcLV05-33B	SRSF4-BGHcLV05-34D	SRSF4-BGHcLV05-34B
Selected	Yes	No	Yes	Yes	Yes	No	Yes	No
Status	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2019-03-13	2022-03-07	2019-03-13
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
				LV41_library_protocol_spikeins			LV41_library_protocol_spikeins
protocol_URL				L-SRSF4-BGHcLV05-33D.pdf			L-SRSF4-BGHcLV05-34D.pdf
ID	3218	6969	7385	7413	7420	7442	7414	7443

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
SRSF4-BGHcLV05-33B_TTAGGC_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1703	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE3	22290
SRSF4-BGHcLV05-33B_TTAGGC_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1703	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE3	22314
SRSF4-BGHcLV05-33B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1703					GRCh38	V40	SRSF4-BGHcLV05-33B_TTAGGC_ACBE67ANXX_L004_001.R1.fastq.gz,SRSF4-BGHcLV05-33B_TTAGGC_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22338
SRSF4-BGHcLV05-33B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1703					GRCh38	V40	SRSF4-BGHcLV05-33B/Aligned.sortedByCoord.out.bam		ENCORE2	22362
SRSF4-BGHcLV05-33B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1703					GRCh38	V40	SRSF4-BGHcLV05-33B/Aligned.sortedByCoord.out.bam		ENCORE2	22386
SRSF4-BGHcLV05-33B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1703					GRCh38	V40	SRSF4-BGHcLV05-33B/Aligned.sortedByCoord.out.bam		ENCORE2	22410
SRSF4-BGHcLV05-33B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1703					GRCh38	V40	SRSF4-BGHcLV05-33B/Aligned.sortedByCoord.out.bam		ENCORE2	22434
SRSF4-BGHcLV05-33B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1703					GRCh38	V40	SRSF4-BGHcLV05-33B_TTAGGC_ACBE67ANXX_L004_001.R1.fastq.gz,SRSF4-BGHcLV05-33B_TTAGGC_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22458
SRSF4-BGHcLV05-33D_S6_R1_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1973	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R1_001.fastq.gz	ENCORE2	27425
SRSF4-BGHcLV05-33D_S6_R2_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1973	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R2_001.fastq.gz	ENCORE2	27453
SRSF4-BGHcLV05-33D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1973					GRCh38	V40	SRSF4-BGHcLV05-33D_S6_R1_001.fastq.gz,SRSF4-BGHcLV05-33D_S6_R2_001.fastq.gz		ENCORE2	27481
SRSF4-BGHcLV05-33D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1973					GRCh38	V40	SRSF4-BGHcLV05-33D/Aligned.sortedByCoord.out.bam		ENCORE2	27509
SRSF4-BGHcLV05-33D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1973					GRCh38	V40	SRSF4-BGHcLV05-33D/Aligned.sortedByCoord.out.bam		ENCORE2	27537
SRSF4-BGHcLV05-33D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1973					GRCh38	V40	SRSF4-BGHcLV05-33D/Aligned.sortedByCoord.out.bam		ENCORE2	27565
SRSF4-BGHcLV05-33D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1973					GRCh38	V40	SRSF4-BGHcLV05-33D/Aligned.sortedByCoord.out.bam		ENCORE2	27593
SRSF4-BGHcLV05-33D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1973					GRCh38	V40	SRSF4-BGHcLV05-33D_S6_R1_001.fastq.gz,SRSF4-BGHcLV05-33D_S6_R2_001.fastq.gz		ENCORE2	27621
SRSF4-BGHcLV05-34B_TGACCA_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1704	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE3	22291
SRSF4-BGHcLV05-34B_TGACCA_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1704	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE3	22315
SRSF4-BGHcLV05-34B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1704					GRCh38	V40	SRSF4-BGHcLV05-34B_TGACCA_ACBE67ANXX_L004_001.R1.fastq.gz,SRSF4-BGHcLV05-34B_TGACCA_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22339
SRSF4-BGHcLV05-34B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1704					GRCh38	V40	SRSF4-BGHcLV05-34B/Aligned.sortedByCoord.out.bam		ENCORE2	22363
SRSF4-BGHcLV05-34B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1704					GRCh38	V40	SRSF4-BGHcLV05-34B/Aligned.sortedByCoord.out.bam		ENCORE2	22387
SRSF4-BGHcLV05-34B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1704					GRCh38	V40	SRSF4-BGHcLV05-34B/Aligned.sortedByCoord.out.bam		ENCORE2	22411
SRSF4-BGHcLV05-34B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1704					GRCh38	V40	SRSF4-BGHcLV05-34B/Aligned.sortedByCoord.out.bam		ENCORE2	22435
SRSF4-BGHcLV05-34B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1704					GRCh38	V40	SRSF4-BGHcLV05-34B_TGACCA_ACBE67ANXX_L004_001.R1.fastq.gz,SRSF4-BGHcLV05-34B_TGACCA_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22459
SRSF4-BGHcLV05-34D_S7_R1_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1974	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R1_001.fastq.gz	ENCORE2	27426
SRSF4-BGHcLV05-34D_S7_R2_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1974	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R2_001.fastq.gz	ENCORE2	27454
SRSF4-BGHcLV05-34D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1974					GRCh38	V40	SRSF4-BGHcLV05-34D_S7_R1_001.fastq.gz,SRSF4-BGHcLV05-34D_S7_R2_001.fastq.gz		ENCORE2	27482
SRSF4-BGHcLV05-34D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1974					GRCh38	V40	SRSF4-BGHcLV05-34D/Aligned.sortedByCoord.out.bam		ENCORE2	27510
SRSF4-BGHcLV05-34D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1974					GRCh38	V40	SRSF4-BGHcLV05-34D/Aligned.sortedByCoord.out.bam		ENCORE2	27538
SRSF4-BGHcLV05-34D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1974					GRCh38	V40	SRSF4-BGHcLV05-34D/Aligned.sortedByCoord.out.bam		ENCORE2	27566
SRSF4-BGHcLV05-34D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1974					GRCh38	V40	SRSF4-BGHcLV05-34D/Aligned.sortedByCoord.out.bam		ENCORE2	27594
SRSF4-BGHcLV05-34D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1974					GRCh38	V40	SRSF4-BGHcLV05-34D_S7_R1_001.fastq.gz,SRSF4-BGHcLV05-34D_S7_R2_001.fastq.gz		ENCORE2	27622