CKAP4 RNA-Seq in K562

General Information


RBP	CKAP4
Cell_Line	K562
Method	shRNA
Exp_Name	CKAP4-BGKLV36-K562
ENCODE_series_ID	ENCSR912NSR
Batch_ID	BGKLV36
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR940GIC
ENCODE_CN_Exp_ID	ENCSR898ABR
Rep1	CKAP4-BGKLV36-9D
Rep2	CKAP4-BGKLV36-10D
CN1	NT-BGKLV36-1D
CN2	NT-BGKLV36-2D
Rep1_qPCR	86.3
Rep2_qPCR	80.9
Rep1_WB
Rep2_WB
Antibody Cat#	A302-256A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB951INP
Status	Released
Project	ENCODE4
ID	881

Experiment Information (Status: Released)

	BGKLV36-9	BGKLV36-10
idx	732	733
TRCN#_or_BGC#	TRCN0000123298	TRCN0000123298
shRNA_or_gRNA_sequence	CTGGATAGGTTGTTTGTGAAA	CTGGATAGGTTGTTTGTGAAA
PAM
Name	CKAP4	CKAP4
Sample_ID	BGKLV36-9	BGKLV36-10
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	CKAP4	CKAP4
qPCR_result	86.3	80.9
Ave_qPCR	83.6
RT-qPCR_primer-F	gagcagttgtcaccacctga
RT-qPCR_primer-R	caaccaaatgcagaagcaga
protein_conc	4297	4030
WB_result
Ave_WB	no band
WB_DONE_date	6/8/16,6/9/16	wes
MW	66kDa
IP	1IP	1IP
antibody_Cat#	A302-256A	A302-256A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0.1	0
Rep2_TPM	0.1	0
Action
Library_start_date	5/11/17	5/11/17
repeat_library	05/11/17	05/11/17
Note
ID	821	822

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
Sample_ID	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
Sample Name	CKAP4-BGKLV36-9B		CKAP4-BGKLV36-10B
Sample Name	CKAP4-BGKLV36-9B	CKAP4-BGKLV36-9D	CKAP4-BGKLV36-10B	CKAP4-BGKLV36-10D
RBP	CKAP4	CKAP4	CKAP4	CKAP4
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	Released	Released	Released
Status_date	2017-11-20	2022-03-07	2017-11-20	2022-03-07
Project	ENCODE3	ENCODE4	ENCODE3	ENCODE4
Note
ID	1332	10439	1331	10440

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
Sample #		59		60
Sample Name	CKAP4-BGKLV36-9B	CKAP4-BGKLV36-9D	CKAP4-BGKLV36-10B	CKAP4-BGKLV36-10D
Sample_Name_Alias	CKAP4-BGKLV36-9B		CKAP4-BGKLV36-10B
Index Well Position	S03	S03	S04	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-05-11	2018-11-19	2017-05-11	2018-11-19
Lib_ID	Lib-170511	Lib-181119	Lib-170511	Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp		288		285
Peak_Molarity		68.50		67.30
libSampleQC_DNA_Well	DNA_Library_set39/set2/C5.png	DNA_Library_set41/set1/D7.png	DNA_Library_set39/set2/D5.png	DNA_Library_set41/set1/C7.png
RIN	9.5	9.5	9.5	9.5
libSample_RNA_Well	RNA_Library_set39/set4/A1.png	RNA_Library_set39/set4/A1.png	RNA_Library_set39/set4/B1.png	RNA_Library_set39/set4/B1.png
SampleQC_method		TapeStation		TapeStation
SampleQC_date		2022-03-01		2022-03-01
Sample_ID	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
RBP	CKAP4	CKAP4	CKAP4	CKAP4
Batch_ID	BGKLV36	BGKLV36	BGKLV36	BGKLV36
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	D	B	D
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE4	ENCODE3	ENCODE4
ID	3029	3236	3028	3237

Sequencing Information

	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
Sample_ID	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
Sample Name	CKAP4-BGKLV36-9B	CKAP4-BGKLV36-9D	CKAP4-BGKLV36-10B	CKAP4-BGKLV36-10D
Pool ID	Pool-170911	Pool-181119	Pool-170911	Pool-181119
LocalServer_folder	set39_K	set41_spikeins	set39_K	set41_spikeins
total_reads	105,000,000	34,499,414	106,000,000	33,565,402
total_aligned_reads	94,690,116	33,573,984	95,728,328	32,719,816
unique_aligned_reads	85,779,614	30,644,922	87,133,918	29,838,994
percent_uniqueAligned	0.81695	0.88827	0.82202	0.88898
correlation_replicates	0.998590	0.997461	0.998590	0.997461
spikein_reads	56	55,746	18	52,536
percent_spikeins		0.00162		0.00157
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1684	1949	1683	1950

Data Submission Information

	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
ENCODE_alias	brenton-graveley:CKAP4-BGKLV36-B	brenton-graveley:CKAP4-BGKLV36-K562_A	brenton-graveley:CKAP4-BGKLV36-D	brenton-graveley:L-CKAP4-BGKLV36-9D	brenton-graveley:CKAP4-BGKLV36-K562	brenton-graveley:CKAP4-BGKLV36-9B	brenton-graveley:L-CKAP4-BGKLV36-10D	brenton-graveley:CKAP4-BGKLV36-10B
ENCODE_accession	ENCSR952OOP	ENCSR718WJL	ENCSR940GIC	ENCLB290XZA	ENCSR912NSR	ENCBS704TWA	ENCLB224ZMX	ENCBS672MAJ
object_type	experiment	experiment	experiment	library	gene_silencing_series	biosample	library	biosample
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-9	BGKLV36-10	BGKLV36-10
Sample Name	CKAP4-BGKLV36-9B	CKAP4-BGKLV36-9B	CKAP4-BGKLV36-9D	CKAP4-BGKLV36-9D	CKAP4-BGKLV36-9D	CKAP4-BGKLV36-9B	CKAP4-BGKLV36-10D	CKAP4-BGKLV36-10B
Selected	Yes	No	Yes	Yes	Yes	No	Yes	No
Status	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2019-03-13	2022-03-07	2019-03-13
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
				LV41_library_protocol_spikeins			LV41_library_protocol_spikeins
protocol_URL				L-CKAP4-BGKLV36-9D.pdf			L-CKAP4-BGKLV36-10D.pdf
ID	3205	6622	7373	7388	7416	7425	7387	7424

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-BGKLV36-9B_TTAGGC_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1684	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1B_ATCACG_ACBE67ANXX_L001_001.R1.fastq.gz,NT-BGKLV36-2B_CGATGT_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE3	22463
CKAP4-BGKLV36-9B_TTAGGC_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1684	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1B_ATCACG_ACBE67ANXX_L001_001.R2.fastq.gz,NT-BGKLV36-2B_CGATGT_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE3	22499
CKAP4-BGKLV36-9B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1684					GRCh38	V40	CKAP4-BGKLV36-9B_TTAGGC_ACBE67ANXX_L001_001.R1.fastq.gz,CKAP4-BGKLV36-9B_TTAGGC_ACBE67ANXX_L001_001.R2.fastq.gz		ENCORE2	22535
CKAP4-BGKLV36-9B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1684					GRCh38	V40	CKAP4-BGKLV36-9B/Aligned.sortedByCoord.out.bam		ENCORE2	22571
CKAP4-BGKLV36-9B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1684					GRCh38	V40	CKAP4-BGKLV36-9B/Aligned.sortedByCoord.out.bam		ENCORE2	22607
CKAP4-BGKLV36-9B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1684					GRCh38	V40	CKAP4-BGKLV36-9B/Aligned.sortedByCoord.out.bam		ENCORE2	22643
CKAP4-BGKLV36-9B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1684					GRCh38	V40	CKAP4-BGKLV36-9B/Aligned.sortedByCoord.out.bam		ENCORE2	22679
CKAP4-BGKLV36-9B_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1684					GRCh38	V40	CKAP4-BGKLV36-9B_TTAGGC_ACBE67ANXX_L001_001.R1.fastq.gz,CKAP4-BGKLV36-9B_TTAGGC_ACBE67ANXX_L001_001.R2.fastq.gz		ENCORE2	22715
CKAP4-BGKLV36-9D_TTAGGC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1949	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1D_ATCACG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV36-2D_NGATGT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27408
CKAP4-BGKLV36-9D_TTAGGC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1949	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1D_ATCACG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV36-2D_NGATGT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27436
CKAP4-BGKLV36-9D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1949					GRCh38	V40	CKAP4-BGKLV36-9D_TTAGGC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,CKAP4-BGKLV36-9D_TTAGGC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27464
CKAP4-BGKLV36-9D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1949					GRCh38	V40	CKAP4-BGKLV36-9D/Aligned.sortedByCoord.out.bam		ENCORE2	27492
CKAP4-BGKLV36-9D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1949					GRCh38	V40	CKAP4-BGKLV36-9D/Aligned.sortedByCoord.out.bam		ENCORE2	27520
CKAP4-BGKLV36-9D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1949					GRCh38	V40	CKAP4-BGKLV36-9D/Aligned.sortedByCoord.out.bam		ENCORE2	27548
CKAP4-BGKLV36-9D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1949					GRCh38	V40	CKAP4-BGKLV36-9D/Aligned.sortedByCoord.out.bam		ENCORE2	27576
CKAP4-BGKLV36-9D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1949					GRCh38	V40	CKAP4-BGKLV36-9D_TTAGGC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,CKAP4-BGKLV36-9D_TTAGGC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27604
CKAP4-BGKLV36-10B_TGACCA_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1683	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1B_ATCACG_ACBE67ANXX_L001_001.R1.fastq.gz,NT-BGKLV36-2B_CGATGT_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE3	22462
CKAP4-BGKLV36-10B_TGACCA_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1683	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1B_ATCACG_ACBE67ANXX_L001_001.R2.fastq.gz,NT-BGKLV36-2B_CGATGT_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE3	22498
CKAP4-BGKLV36-10B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1683					GRCh38	V40	CKAP4-BGKLV36-10B_TGACCA_ACBE67ANXX_L001_001.R1.fastq.gz,CKAP4-BGKLV36-10B_TGACCA_ACBE67ANXX_L001_001.R2.fastq.gz		ENCORE2	22534
CKAP4-BGKLV36-10B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1683					GRCh38	V40	CKAP4-BGKLV36-10B/Aligned.sortedByCoord.out.bam		ENCORE2	22570
CKAP4-BGKLV36-10B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1683					GRCh38	V40	CKAP4-BGKLV36-10B/Aligned.sortedByCoord.out.bam		ENCORE2	22606
CKAP4-BGKLV36-10B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1683					GRCh38	V40	CKAP4-BGKLV36-10B/Aligned.sortedByCoord.out.bam		ENCORE2	22642
CKAP4-BGKLV36-10B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1683					GRCh38	V40	CKAP4-BGKLV36-10B/Aligned.sortedByCoord.out.bam		ENCORE2	22678
CKAP4-BGKLV36-10B_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1683					GRCh38	V40	CKAP4-BGKLV36-10B_TGACCA_ACBE67ANXX_L001_001.R1.fastq.gz,CKAP4-BGKLV36-10B_TGACCA_ACBE67ANXX_L001_001.R2.fastq.gz		ENCORE2	22714
CKAP4-BGKLV36-10D_TGACCA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1950	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1D_ATCACG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV36-2D_NGATGT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27407
CKAP4-BGKLV36-10D_TGACCA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1950	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1D_ATCACG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV36-2D_NGATGT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27435
CKAP4-BGKLV36-10D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1950					GRCh38	V40	CKAP4-BGKLV36-10D_TGACCA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,CKAP4-BGKLV36-10D_TGACCA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27463
CKAP4-BGKLV36-10D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1950					GRCh38	V40	CKAP4-BGKLV36-10D/Aligned.sortedByCoord.out.bam		ENCORE2	27491
CKAP4-BGKLV36-10D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1950					GRCh38	V40	CKAP4-BGKLV36-10D/Aligned.sortedByCoord.out.bam		ENCORE2	27519
CKAP4-BGKLV36-10D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1950					GRCh38	V40	CKAP4-BGKLV36-10D/Aligned.sortedByCoord.out.bam		ENCORE2	27547
CKAP4-BGKLV36-10D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1950					GRCh38	V40	CKAP4-BGKLV36-10D/Aligned.sortedByCoord.out.bam		ENCORE2	27575
CKAP4-BGKLV36-10D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1950					GRCh38	V40	CKAP4-BGKLV36-10D_TGACCA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,CKAP4-BGKLV36-10D_TGACCA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27603