CKAP4 RNA-Seq in HepG2

General Information


RBP	CKAP4
Cell_Line	HepG2
Method	shRNA
Exp_Name	CKAP4-BGHLV31-HepG2
ENCODE_series_ID	ENCSR707MIU
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR269SJB
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	CKAP4_BGHLV31-23
Rep2	CKAP4_BGHLV31-24
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	82.6
Rep2_qPCR	83.7
Rep1_WB	56.2
Rep2_WB	54.7
Antibody Cat#	A302-256A
Antibody Lot#	A302-256A
Antibody DCC ID	ENCAB951INP
Status	Released
Project	ENCODE3
ID	693

Experiment Information (Status: Released)

	BGHLV31-23	BGHLV31-24
idx	771	772
TRCN#_or_BGC#	TRCN0000123298	TRCN0000123298
shRNA_or_gRNA_sequence	CTGGATAGGTTGTTTGTGAAA	CTGGATAGGTTGTTTGTGAAA
PAM
Name	CKAP4	CKAP4
Sample_ID	BGHLV31-23	BGHLV31-24
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	CKAP4	CKAP4
qPCR_result	82.6	83.7
Ave_qPCR	83.2
RT-qPCR_primer-F	gagcagttgtcaccacctga
RT-qPCR_primer-R	caaccaaatgcagaagcaga
protein_conc	3278	3884
WB_result	56.2	54.7
Ave_WB	55.4
WB_DONE_date	12/2/2015
MW	66kDa
IP	1IP	1IP
antibody_Cat#	A302-256A	A302-256A
Antibody DCC ID	ENCAB951INP	ENCAB951INP
submitted_to_DCC_date	12/7/2015
Rep1_TPM	59.3	0
Rep2_TPM	68.7	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2864	2865

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CKAP4	Product_ID: A302-256A Lot_ID: 1 Source: Bethyl Labs Target Name: CKAP4-human

Experiment Status

	BGHLV31-23	BGHLV31-24
Sample_ID	BGHLV31-23	BGHLV31-24
Sample Name	CKAP4_BGHLV31-23	CKAP4_BGHLV31-24
Sample Name	CKAP4_BGHLV31-23	CKAP4_BGHLV31-24
RBP	CKAP4	CKAP4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1113	1114

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-23	BGHLV31-24
Sample #
Sample Name	CKAP4-BGHLV31-23	CKAP4-BGHLV31-24
Sample_Name_Alias	CKAP4_BGHLV31-23	CKAP4_BGHLV31-24
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/G5.png	DNA_Library_LV31-21B/set1/H5.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G8.png	RNA_Library_LV29-30-31-32/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-23	BGHLV31-24
RBP	CKAP4	CKAP4
Batch_ID	BGHLV31	BGHLV31
WB_result	56.200	54.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2810	2811

Sequencing Information

	BGHLV31-23	BGHLV31-24
Sample_ID	BGHLV31-23	BGHLV31-24
Sample Name	CKAP4_BGHLV31-23	CKAP4_BGHLV31-24
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	63,880,264	62,293,952
total_aligned_reads	57,372,912	56,019,920
unique_aligned_reads	53,899,174	52,667,136
percent_uniqueAligned	0.84375	0.84546
correlation_replicates	0.999371	0.999371
spikein_reads	295,740	292,468
percent_spikeins	0.00463	0.00469
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1459	1460

Data Submission Information

	BGHLV31-23	BGHLV31-23
ENCODE_alias	brenton-graveley:CKAP4_BGHLV31	brenton-graveley:CKAP4-BGHLV31-HepG2
ENCODE_accession	ENCSR269SJB	ENCSR707MIU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-23	BGHLV31-23
Sample Name	CKAP4_BGHLV31-23	CKAP4_BGHLV31-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3089	6621

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
CKAP4_BGHLV31-23_ATGTCA_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1459	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20974
CKAP4_BGHLV31-23_ATGTCA_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1459	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21000
CKAP4_BGHLV31-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1459					GRCh38	V40	CKAP4_BGHLV31-23_ATGTCA_L005_001.R1.fastq.gz,CKAP4_BGHLV31-23_ATGTCA_L005_001.R2.fastq.gz		ENCORE2	21034
CKAP4_BGHLV31-23_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1459					GRCh38	V40	CKAP4_BGHLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	21060
CKAP4_BGHLV31-23_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1459					GRCh38	V40	CKAP4_BGHLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	21086
CKAP4_BGHLV31-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1459					GRCh38	V40	CKAP4_BGHLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	21112
CKAP4_BGHLV31-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1459					GRCh38	V40	CKAP4_BGHLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	21138
CKAP4_BGHLV31-23_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1459					GRCh38	V40	CKAP4_BGHLV31-23_ATGTCA_L005_001.R1.fastq.gz,CKAP4_BGHLV31-23_ATGTCA_L005_001.R2.fastq.gz		ENCORE2	21164
CKAP4_BGHLV31-24_CCGTCC_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1460	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20975
CKAP4_BGHLV31-24_CCGTCC_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1460	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21001
CKAP4_BGHLV31-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1460					GRCh38	V40	CKAP4_BGHLV31-24_CCGTCC_L005_001.R1.fastq.gz,CKAP4_BGHLV31-24_CCGTCC_L005_001.R2.fastq.gz		ENCORE2	21035
CKAP4_BGHLV31-24_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1460					GRCh38	V40	CKAP4_BGHLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	21061
CKAP4_BGHLV31-24_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1460					GRCh38	V40	CKAP4_BGHLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	21087
CKAP4_BGHLV31-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1460					GRCh38	V40	CKAP4_BGHLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	21113
CKAP4_BGHLV31-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1460					GRCh38	V40	CKAP4_BGHLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	21139
CKAP4_BGHLV31-24_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1460					GRCh38	V40	CKAP4_BGHLV31-24_CCGTCC_L005_001.R1.fastq.gz,CKAP4_BGHLV31-24_CCGTCC_L005_001.R2.fastq.gz		ENCORE2	21165