SERBP1 RNA-Seq in K562

General Information


RBP	SERBP1
Cell_Line	K562
Method	shRNA
Exp_Name	SERBP1-BGKLV19-K562
ENCODE_series_ID	ENCSR284WTC
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR925RNE
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	SERBP1_BGKLV19_49B
Rep2	SERBP1_BGKLV19_50B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	76.2
Rep2_qPCR	84.0
Rep1_WB	80.8
Rep2_WB	78.4
Antibody Cat#	RN056PW
Antibody Lot#	RN056PW
Antibody DCC ID	ENCAB229RIQ
Status	Released
Project	ENCODE3
ID	481

Experiment Information (Status: Released)

	BGKLV19-49	BGKLV19-50
idx	256	257
TRCN#_or_BGC#	TRCN0000160878	TRCN0000160878
shRNA_or_gRNA_sequence	GATTCGGTTATGGACCATCAT	GATTCGGTTATGGACCATCAT
PAM
Name	SERBP1	SERBP1
Sample_ID	BGKLV19-49	BGKLV19-50
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	SERBP1	SERBP1
qPCR_result	76.2	84.0
Ave_qPCR	80.1
RT-qPCR_primer-F	gcaggaccgacaagtcaagt
RT-qPCR_primer-R	gcatccagttaagccagagc
protein_conc	2430	2766
WB_result	80.8	78.4
Ave_WB	79.6
WB_DONE_date	3/2/2015
MW
IP	1MW	1MW
antibody_Cat#	RN056PW	RN056PW
Antibody DCC ID	ENCAB229RIQ	ENCAB229RIQ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	74.8332757	0
Rep2_TPM	49.5601715	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	281	282

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

	BGKLV19-49	BGKLV19-50
Sample_ID	BGKLV19-49	BGKLV19-50
Sample Name	SERBP1_BGKLV19_49B	SERBP1_BGKLV19_50B
Sample Name	SERBP1_BGKLV19_49B	SERBP1_BGKLV19_50B
RBP	SERBP1	SERBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	696	697

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-49	BGKLV19-50
Sample #
Sample Name	SERBP1-BGKLV19-49B	SERBP1-BGKLV19-50B
Sample_Name_Alias	SERBP1_BGKLV19_49B	SERBP1_BGKLV19_50B
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A11.png	DNA_Library_LV18-19/set1/B11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E5.png	RNA_Library_LV19-21-24/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-49	BGKLV19-50
RBP	SERBP1	SERBP1
Batch_ID	BGKLV19	BGKLV19
WB_result	80.800	78.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2380	2381

Sequencing Information

	BGKLV19-49	BGKLV19-50
Sample_ID	BGKLV19-49	BGKLV19-50
Sample Name	SERBP1_BGKLV19_49B	SERBP1_BGKLV19_50B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	33,170,000	41,960,000
total_aligned_reads	31,250,544	39,804,952
unique_aligned_reads	28,390,050	36,076,680
percent_uniqueAligned	0.85590	0.85979
correlation_replicates	0.998421	0.998421
spikein_reads	129,712	116,296
percent_spikeins	0.00391	0.00277
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1022	1023

Data Submission Information

	BGKLV19-49	BGKLV19-49
ENCODE_alias	brenton-graveley:SERBP1_BGKLV19	brenton-graveley:SERBP1-BGKLV19-K562
ENCODE_accession	ENCSR925RNE	ENCSR284WTC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-49	BGKLV19-49
Sample Name	SERBP1_BGKLV19_49B	SERBP1_BGKLV19_49B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2896	6937

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_BGKLV19_49B_GATCAG_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1022	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15138
SERBP1_BGKLV19_49B_GATCAG_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1022	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15196
SERBP1_BGKLV19_49B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1022					GRCh38	V40	SERBP1_BGKLV19_49B_GATCAG_L006_R1_001.fastq.gz,SERBP1_BGKLV19_49B_GATCAG_L006_R2_001.fastq.gz		ENCORE2	15254
SERBP1_BGKLV19_49B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1022					GRCh38	V40	SERBP1_BGKLV19_49B/Aligned.sortedByCoord.out.bam		ENCORE2	15325
SERBP1_BGKLV19_49B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1022					GRCh38	V40	SERBP1_BGKLV19_49B/Aligned.sortedByCoord.out.bam		ENCORE2	15383
SERBP1_BGKLV19_49B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1022					GRCh38	V40	SERBP1_BGKLV19_49B/Aligned.sortedByCoord.out.bam		ENCORE2	15441
SERBP1_BGKLV19_49B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1022					GRCh38	V40	SERBP1_BGKLV19_49B/Aligned.sortedByCoord.out.bam		ENCORE2	15499
SERBP1_BGKLV19_49B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1022					GRCh38	V40	SERBP1_BGKLV19_49B_GATCAG_L006_R1_001.fastq.gz,SERBP1_BGKLV19_49B_GATCAG_L006_R2_001.fastq.gz		ENCORE2	16396
SERBP1_BGKLV19_50B_TAGCTT_L006_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1023	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15139
SERBP1_BGKLV19_50B_TAGCTT_L006_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1023	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15197
SERBP1_BGKLV19_50B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1023					GRCh38	V40	SERBP1_BGKLV19_50B_TAGCTT_L006_R1_001.fastq.gz,SERBP1_BGKLV19_50B_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	15255
SERBP1_BGKLV19_50B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1023					GRCh38	V40	SERBP1_BGKLV19_50B/Aligned.sortedByCoord.out.bam		ENCORE2	15326
SERBP1_BGKLV19_50B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1023					GRCh38	V40	SERBP1_BGKLV19_50B/Aligned.sortedByCoord.out.bam		ENCORE2	15384
SERBP1_BGKLV19_50B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1023					GRCh38	V40	SERBP1_BGKLV19_50B/Aligned.sortedByCoord.out.bam		ENCORE2	15442
SERBP1_BGKLV19_50B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1023					GRCh38	V40	SERBP1_BGKLV19_50B/Aligned.sortedByCoord.out.bam		ENCORE2	15500
SERBP1_BGKLV19_50B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1023					GRCh38	V40	SERBP1_BGKLV19_50B_TAGCTT_L006_R1_001.fastq.gz,SERBP1_BGKLV19_50B_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	16397