CPEB4 RNA-Seq in K562

General Information


RBP	CPEB4
Cell_Line	K562
Method	shRNA
Exp_Name	CPEB4-BGKLV25-K562
ENCODE_series_ID	ENCSR730QGA
Batch_ID	BGKLV25
Pool ID	Pool-160425
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR795VAK
ENCODE_CN_Exp_ID	ENCSR031RRO
Rep1	CPEB4_BGKLV25-7B
Rep2	CPEB4_BGKLV25-8B
CN1	NT_BGKLV25-1B
CN2	NT_BGKLV25-2B
Rep1_qPCR	52.6
Rep2_qPCR	61.1
Rep1_WB	75.1
Rep2_WB	88.2
Antibody Cat#	RN040PW
Antibody Lot#	RN040PW
Antibody DCC ID	ENCAB442TOR
Status	Released
Project	ENCODE3
ID	614

Experiment Information (Status: NotSatisfied)

	BGKLV25-7	BGKLV25-8
idx	408	409
TRCN#_or_BGC#	TRCN0000150825	TRCN0000150825
shRNA_or_gRNA_sequence	GCTGTTGGAAAGACTTGATAA	GCTGTTGGAAAGACTTGATAA
PAM
Name	CPEB4	CPEB4
Sample_ID	BGKLV25-7	BGKLV25-8
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	CPEB4	CPEB4
qPCR_result	52.6	61.1
Ave_qPCR	56.8
RT-qPCR_primer-F	ttgcctccagacattgatga
RT-qPCR_primer-R	agctttatgaggccaatcca
protein_conc	3603	3961
WB_result	75.1	88.2
Ave_WB	81.6
WB_DONE_date	2/22/2016
MW	80kDa	wes
IP	0.5MB	0.5MB
antibody_Cat#	RN040PW	RN040PW
Antibody DCC ID	ENCAB442TOR	ENCAB442TOR
submitted_to_DCC_date	3/8/2016
Rep1_TPM	1.45895602	0
Rep2_TPM	1.6867368	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	467	468

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPEB4	Product_ID: RN040PW Lot_ID: 1 Source: MBLI Target Name: CPEB4-human

Experiment Status

	BGKLV25-7	BGKLV25-7	BGKLV25-8	BGKLV25-8
Sample_ID	BGKLV25-7	BGKLV25-7	BGKLV25-8	BGKLV25-8
Sample Name	CPEB4_BGKLV25-7	CPEB4_BGKLV25-7B	CPEB4_BGKLV25-8	CPEB4_BGKLV25-8B
Sample Name	CPEB4_BGKLV25-7	CPEB4_BGKLV25-7B	CPEB4_BGKLV25-8	CPEB4_BGKLV25-8B
RBP	CPEB4	CPEB4	CPEB4	CPEB4
Cell_Line	K562	K562	K562	K562
Exp UID
Status	NotSatisfied	Released	NotSatisfied	Released
Status_date	2015-12-08	2016-09-24	2015-12-08	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note	Bad Correlation between replicates		Bad Correlation between replicates
ID	24	1195	25	1196

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-7	BGKLV25-7	BGKLV25-8	BGKLV25-8
Sample #
Sample Name	CPEB4-BGKLV25-7	CPEB4-BGKLV25-7B	CPEB4-BGKLV25-8	CPEB4-BGKLV25-8B
Sample_Name_Alias	CPEB4_BGKLV25-7	CPEB4_BGKLV25-7B	CPEB4_BGKLV25-8	CPEB4_BGKLV25-8B
Index Well Position	S13	S03	S14	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2016-03-04	2015-06-23	2016-03-04
Lib_ID	Lib-150623	Lib-160304	Lib-150623	Lib-160304
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set2/B2.png	DNA_Library_LV33-34-25B-32/set2/E1.png	DNA_Library_LV24-25-26/set2/C2.png	DNA_Library_LV33-34-25B-32/set1/D5.png
RIN	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E9.png	RNA_Library_LV22-23-25/set1/E9.png	RNA_Library_LV22-23-25/set1/F9.png	RNA_Library_LV22-23-25/set1/F9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-7	BGKLV25-7	BGKLV25-8	BGKLV25-8
RBP	CPEB4	CPEB4	CPEB4	CPEB4
Batch_ID	BGKLV25	BGKLV25	BGKLV25	BGKLV25
WB_result	75.100	75.100	88.200	88.200
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2598	2894	2599	2895

Sequencing Information

	BGKLV25-7	BGKLV25-7	BGKLV25-8	BGKLV25-8
Sample_ID	BGKLV25-7	BGKLV25-7	BGKLV25-8	BGKLV25-8
Sample Name	CPEB4_BGKLV25-7	CPEB4_BGKLV25-7B	CPEB4_BGKLV25-8	CPEB4_BGKLV25-8B
Pool ID	Pool-151101	Pool-160425	Pool-151101	Pool-160425
LocalServer_folder	set25	set25	set25	set25
total_reads	137,827,248	116,601,948	14,503,136	72,943,670
total_aligned_reads	140,095,670	87,223,782	12,776,548	55,272,970
unique_aligned_reads	128,114,604	79,637,106	11,736,488	50,442,670
percent_uniqueAligned	0.92953	0.68298	0.80924	0.69153
correlation_replicates	0.864298	0.998400	0.864298	0.998400
spikein_reads	666,728	337,208	13,820	226,506
percent_spikeins	0.00484	0.00289	0.00095	0.00311
original_ReadLength	100	100	100	100
QC_Status	BadCorrelation	Submitted	BadCorrelation	Submitted
ID	1240	1543	1241	1544

Data Submission Information

	BGKLV25-7	BGKLV25-7
ENCODE_alias	brenton-graveley:CPEB4_BGKLV25	brenton-graveley:CPEB4-BGKLV25-K562
ENCODE_accession	ENCSR795VAK	ENCSR730QGA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-7	BGKLV25-7
Sample Name	CPEB4_BGKLV25-7B	CPEB4_BGKLV25-7B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3137	6625

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
CPEB4_BGKLV25-7B_TTAGGC_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1543	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE3	19564
CPEB4_BGKLV25-7B_TTAGGC_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1543	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE3	19600
CPEB4_BGKLV25-7B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1543					GRCh38	V40	CPEB4_BGKLV25-7B_TTAGGC_L008_001.R1.fastq.gz,CPEB4_BGKLV25-7B_TTAGGC_L008_001.R2.fastq.gz		ENCORE2	19636
CPEB4_BGKLV25-7B_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1543					GRCh38	V40	CPEB4_BGKLV25-7B/Aligned.sortedByCoord.out.bam		ENCORE2	19672
CPEB4_BGKLV25-7B_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1543					GRCh38	V40	CPEB4_BGKLV25-7B/Aligned.sortedByCoord.out.bam		ENCORE2	19708
CPEB4_BGKLV25-7B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1543					GRCh38	V40	CPEB4_BGKLV25-7B/Aligned.sortedByCoord.out.bam		ENCORE2	19744
CPEB4_BGKLV25-7B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1543					GRCh38	V40	CPEB4_BGKLV25-7B/Aligned.sortedByCoord.out.bam		ENCORE2	19780
CPEB4_BGKLV25-7B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1543					GRCh38	V40	CPEB4_BGKLV25-7B_TTAGGC_L008_001.R1.fastq.gz,CPEB4_BGKLV25-7B_TTAGGC_L008_001.R2.fastq.gz		ENCORE2	19970
CPEB4_BGKLV25-8B_TGACCA_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1544	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE3	19565
CPEB4_BGKLV25-8B_TGACCA_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1544	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE3	19601
CPEB4_BGKLV25-8B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1544					GRCh38	V40	CPEB4_BGKLV25-8B_TGACCA_L008_001.R1.fastq.gz,CPEB4_BGKLV25-8B_TGACCA_L008_001.R2.fastq.gz		ENCORE2	19637
CPEB4_BGKLV25-8B_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1544					GRCh38	V40	CPEB4_BGKLV25-8B/Aligned.sortedByCoord.out.bam		ENCORE2	19673
CPEB4_BGKLV25-8B_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1544					GRCh38	V40	CPEB4_BGKLV25-8B/Aligned.sortedByCoord.out.bam		ENCORE2	19709
CPEB4_BGKLV25-8B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1544					GRCh38	V40	CPEB4_BGKLV25-8B/Aligned.sortedByCoord.out.bam		ENCORE2	19745
CPEB4_BGKLV25-8B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1544					GRCh38	V40	CPEB4_BGKLV25-8B/Aligned.sortedByCoord.out.bam		ENCORE2	19781
CPEB4_BGKLV25-8B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1544					GRCh38	V40	CPEB4_BGKLV25-8B_TGACCA_L008_001.R1.fastq.gz,CPEB4_BGKLV25-8B_TGACCA_L008_001.R2.fastq.gz		ENCORE2	19971