SRFBP1 RNA-Seq in HepG2

General Information


RBP	SRFBP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRFBP1-BGHLV37-HepG2
ENCODE_series_ID	ENCSR267PMJ
Batch_ID	BGHLV37
Pool ID	Pool-161129
Local_Set_Name	set37
ENCODE_KD_Exp_ID	ENCSR153GKS
ENCODE_CN_Exp_ID	ENCSR997HCQ
Rep1	SRFBP1_BGHLV37-57
Rep2	SRFBP1_BGHLV37-58
CN1	NT_BGHLV37-1
CN2	NT_BGHLV37-2
Rep1_qPCR	60.7
Rep2_qPCR	54.8
Rep1_WB	67.1
Rep2_WB	68.9
Antibody Cat#	A303-044A
Antibody Lot#	A303-044A
Antibody DCC ID	ENCAB974FYT
Status	Released
Project	ENCODE3
ID	753

Experiment Information (Status: Released)

	BGHLV37-57	BGHLV37-58
idx	969	970
TRCN#_or_BGC#	TRCN0000168057	TRCN0000168057
shRNA_or_gRNA_sequence	CCAGATTCTACTGCAACTGAA	CCAGATTCTACTGCAACTGAA
PAM
Name	SRFBP1	SRFBP1
Sample_ID	BGHLV37-57	BGHLV37-58
transduction_Date	9/1/16	9/1/16
days
RBP_name	SRFBP1	SRFBP1
qPCR_result	60.7	54.8
Ave_qPCR	57.7
RT-qPCR_primer-F	aaatttcaaagaacaggctcca
RT-qPCR_primer-R	tgattcttgatctgaggctcatt
protein_conc	5222	4653
WB_result	67.1	68.9
Ave_WB	68.0
WB_DONE_date	9/19/16
MW	49kDa
IP	1	1
antibody_Cat#	A303-044A	A303-044A
Antibody DCC ID	ENCAB974FYT	ENCAB974FYT
submitted_to_DCC_date	10/26/16
Rep1_TPM	5.8	0
Rep2_TPM	4.8	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	3062	3063

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRFBP1	Product_ID: A303-044A Lot_ID: 1 Source: Bethyl Labs Target Name: SRFBP1-human

Experiment Status

	BGHLV37-57	BGHLV37-58
Sample_ID	BGHLV37-57	BGHLV37-58
Sample Name	SRFBP1_BGHLV37-57	SRFBP1_BGHLV37-58
Sample Name	SRFBP1_BGHLV37-57	SRFBP1_BGHLV37-58
RBP	SRFBP1	SRFBP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1301	1302

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-57	BGHLV37-58
Sample #
Sample Name	SRFBP1-BGHLV37-57	SRFBP1-BGHLV37-58
Sample_Name_Alias	SRFBP1_BGHLV37-57	SRFBP1_BGHLV37-58
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/C4.png	DNA_Library_LV37-38/set1/D4.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV37_38/set1/C2.png	RNA_Library_LV37_38/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV37-57	BGHLV37-58
RBP	SRFBP1	SRFBP1
Batch_ID	BGHLV37	BGHLV37
WB_result	67.100	68.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2988	2989

Sequencing Information

	BGHLV37-57	BGHLV37-58
Sample_ID	BGHLV37-57	BGHLV37-58
Sample Name	SRFBP1_BGHLV37-57	SRFBP1_BGHLV37-58
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set37	set37
total_reads	110,000,000	71,831,734
total_aligned_reads	100,413,102	65,897,118
unique_aligned_reads	93,830,938	61,700,298
percent_uniqueAligned	0.85301	0.85896
correlation_replicates	0.999654	0.999654
spikein_reads	465,270	241,658
percent_spikeins	0.00423	0.00336
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1637	1638

Data Submission Information

	BGHLV37-57	BGHLV37-57
ENCODE_alias	brenton-graveley:SRFBP1_BGHLV37	brenton-graveley:SRFBP1-BGHLV37-HepG2
ENCODE_accession	ENCSR153GKS	ENCSR267PMJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-57	BGHLV37-57
Sample Name	SRFBP1_BGHLV37-57	SRFBP1_BGHLV37-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3190	6961

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
SRFBP1_BGHLV37-57_TTAGGC_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1637	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22044
SRFBP1_BGHLV37-57_TTAGGC_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1637	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22060
SRFBP1_BGHLV37-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1637					GRCh38	V40	SRFBP1_BGHLV37-57_TTAGGC_L006_001.R1.fastq.gz,SRFBP1_BGHLV37-57_TTAGGC_L006_001.R2.fastq.gz		ENCORE2	22076
SRFBP1_BGHLV37-57_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1637					GRCh38	V40	SRFBP1_BGHLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	22092
SRFBP1_BGHLV37-57_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1637					GRCh38	V40	SRFBP1_BGHLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	22108
SRFBP1_BGHLV37-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1637					GRCh38	V40	SRFBP1_BGHLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	22124
SRFBP1_BGHLV37-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1637					GRCh38	V40	SRFBP1_BGHLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	22140
SRFBP1_BGHLV37-57_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1637					GRCh38	V40	SRFBP1_BGHLV37-57_TTAGGC_L006_001.R1.fastq.gz,SRFBP1_BGHLV37-57_TTAGGC_L006_001.R2.fastq.gz		ENCORE2	22156
SRFBP1_BGHLV37-58_TGACCA_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1638	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22045
SRFBP1_BGHLV37-58_TGACCA_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1638	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22061
SRFBP1_BGHLV37-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1638					GRCh38	V40	SRFBP1_BGHLV37-58_TGACCA_L006_001.R1.fastq.gz,SRFBP1_BGHLV37-58_TGACCA_L006_001.R2.fastq.gz		ENCORE2	22077
SRFBP1_BGHLV37-58_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1638					GRCh38	V40	SRFBP1_BGHLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	22093
SRFBP1_BGHLV37-58_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1638					GRCh38	V40	SRFBP1_BGHLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	22109
SRFBP1_BGHLV37-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1638					GRCh38	V40	SRFBP1_BGHLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	22125
SRFBP1_BGHLV37-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1638					GRCh38	V40	SRFBP1_BGHLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	22141
SRFBP1_BGHLV37-58_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1638					GRCh38	V40	SRFBP1_BGHLV37-58_TGACCA_L006_001.R1.fastq.gz,SRFBP1_BGHLV37-58_TGACCA_L006_001.R2.fastq.gz		ENCORE2	22157