SERBP1 RNA-Seq in HepG2

General Information


RBP	SERBP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SERBP1-BGHLV16-HepG2
ENCODE_series_ID	ENCSR779VTD
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR820ROH
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	SERBP1_BGHLV16_51
Rep2	SERBP1_BGHLV16_52
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	67.5
Rep2_qPCR	67.7
Rep1_WB	73.9
Rep2_WB	75.7
Antibody Cat#	RN056PW
Antibody Lot#	RN056PW
Antibody DCC ID	ENCAB229RIQ
Status	Released
Project	ENCODE3
ID	424

Experiment Information (Status: Released)

	BGHLV16-51	BGHLV16-52
idx	219	220
TRCN#_or_BGC#	TRCN0000160878	TRCN0000160878
shRNA_or_gRNA_sequence	GATTCGGTTATGGACCATCAT	GATTCGGTTATGGACCATCAT
PAM
Name	SERBP1	SERBP1
Sample_ID	BGHLV16-51	BGHLV16-52
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	SERBP1	SERBP1
qPCR_result	67.5	67.7
Ave_qPCR	67.6
RT-qPCR_primer-F	gcaggaccgacaagtcaagt
RT-qPCR_primer-R	gcatccagttaagccagagc
protein_conc	2589	2951
WB_result	73.9	75.7
Ave_WB	74.8
WB_DONE_date	3/2/2015
MW	45kDa
IP	1MW	1MW
antibody_Cat#	RN056PW	RN056PW
Antibody DCC ID	ENCAB229RIQ	ENCAB229RIQ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	87.3	0
Rep2_TPM	68.2	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2284	2285

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SERBP1	Product_ID: RN056PW Lot_ID: 1 Source: MBLI Target Name: SERBP1-human

Experiment Status

	BGHLV16-51	BGHLV16-52
Sample_ID	BGHLV16-51	BGHLV16-52
Sample Name	SERBP1_BGHLV16_51	SERBP1_BGHLV16_52
Sample Name	SERBP1_BGHLV16_51	SERBP1_BGHLV16_52
RBP	SERBP1	SERBP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	574	575

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-51	BGHLV16-52
Sample #
Sample Name	SERBP1-BGHLV16-51	SERBP1-BGHLV16-52
Sample_Name_Alias	SERBP1_BGHLV16_51	SERBP1_BGHLV16_52
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/G8.png	DNA_Library_LV16-17/set1/H8.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E2.png	RNA_Library_LV16-17-18/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-51	BGHLV16-52
RBP	SERBP1	SERBP1
Batch_ID	BGHLV16	BGHLV16
WB_result	73.900	75.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2258	2259

Sequencing Information

	BGHLV16-51	BGHLV16-52
Sample_ID	BGHLV16-51	BGHLV16-52
Sample Name	SERBP1_BGHLV16_51	SERBP1_BGHLV16_52
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	66,380,000	43,800,000
total_aligned_reads	59,666,250	39,157,470
unique_aligned_reads	56,356,152	36,988,390
percent_uniqueAligned	0.84899	0.84448
correlation_replicates	0.999703	0.999703
spikein_reads	178,118	140,218
percent_spikeins	0.00268	0.00320
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	900	901

Data Submission Information

	BGHLV16-51	BGHLV16-51
ENCODE_alias	brenton-graveley:SERBP1_BGHLV16	brenton-graveley:SERBP1-BGHLV16-HepG2
ENCODE_accession	ENCSR820ROH	ENCSR779VTD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-51	BGHLV16-51
Sample Name	SERBP1_BGHLV16_51	SERBP1_BGHLV16_51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2855	6936

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
SERBP1_BGHLV16_51_ACTGAT_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	900	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14300
SERBP1_BGHLV16_51_ACTGAT_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	900	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14326
SERBP1_BGHLV16_51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	900					GRCh38	V40	SERBP1_BGHLV16_51_ACTGAT_L008_R1_001.fastq.gz,SERBP1_BGHLV16_51_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	14352
SERBP1_BGHLV16_51_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	900					GRCh38	V40	SERBP1_BGHLV16_51/Aligned.sortedByCoord.out.bam		ENCORE2	14378
SERBP1_BGHLV16_51_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	900					GRCh38	V40	SERBP1_BGHLV16_51/Aligned.sortedByCoord.out.bam		ENCORE2	14404
SERBP1_BGHLV16_51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	900					GRCh38	V40	SERBP1_BGHLV16_51/Aligned.sortedByCoord.out.bam		ENCORE2	14430
SERBP1_BGHLV16_51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	900					GRCh38	V40	SERBP1_BGHLV16_51/Aligned.sortedByCoord.out.bam		ENCORE2	14456
SERBP1_BGHLV16_51_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	900					GRCh38	V40	SERBP1_BGHLV16_51_ACTGAT_L008_R1_001.fastq.gz,SERBP1_BGHLV16_51_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	14482
SERBP1_BGHLV16_52_ATTCCT_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	901	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14301
SERBP1_BGHLV16_52_ATTCCT_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	901	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14327
SERBP1_BGHLV16_52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	901					GRCh38	V40	SERBP1_BGHLV16_52_ATTCCT_L008_R1_001.fastq.gz,SERBP1_BGHLV16_52_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	14353
SERBP1_BGHLV16_52_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	901					GRCh38	V40	SERBP1_BGHLV16_52/Aligned.sortedByCoord.out.bam		ENCORE2	14379
SERBP1_BGHLV16_52_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	901					GRCh38	V40	SERBP1_BGHLV16_52/Aligned.sortedByCoord.out.bam		ENCORE2	14405
SERBP1_BGHLV16_52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	901					GRCh38	V40	SERBP1_BGHLV16_52/Aligned.sortedByCoord.out.bam		ENCORE2	14431
SERBP1_BGHLV16_52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	901					GRCh38	V40	SERBP1_BGHLV16_52/Aligned.sortedByCoord.out.bam		ENCORE2	14457
SERBP1_BGHLV16_52_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	901					GRCh38	V40	SERBP1_BGHLV16_52_ATTCCT_L008_R1_001.fastq.gz,SERBP1_BGHLV16_52_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	14483