CCDC124 RNA-Seq in K562

General Information


RBP	CCDC124
Cell_Line	K562
Method	shRNA
Exp_Name	CCDC124-BGKLV32-K562
ENCODE_series_ID	ENCSR875BHL
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR874ZLI
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	CCDC124_BGKLV32-13
Rep2	CCDC124_BGKLV32-14
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	81.8
Rep2_qPCR	83.3
Rep1_WB	63.6
Rep2_WB	63.6
Antibody Cat#	A301-835A
Antibody Lot#	A301-835A
Antibody DCC ID	ENCAB759HYT
Status	Released
Project	ENCODE3
ID	706

Experiment Information (Status: Released)

	BGKLV32-13	BGKLV32-14
idx	612	613
TRCN#_or_BGC#	TRCN0000242988	TRCN0000242988
shRNA_or_gRNA_sequence	ACTGGAAGGACGACGACAAAC	ACTGGAAGGACGACGACAAAC
PAM
Name	CCDC124	CCDC124
Sample_ID	BGKLV32-13	BGKLV32-14
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	CCDC124	CCDC124
qPCR_result	81.8	83.3
Ave_qPCR	82.5
RT-qPCR_primer-F	ggaggactccaagctcaagg
RT-qPCR_primer-R	cagatggctcttggctttct
protein_conc	3199	3109
WB_result	63.6	63.6
Ave_WB	63.6
WB_DONE_date	11/9/2015
MW	26kDa
IP	1IP	1IP
antibody_Cat#	A301-835A	A301-835A
Antibody DCC ID	ENCAB759HYT	ENCAB759HYT
submitted_to_DCC_date	12/7/2015
Rep1_TPM	38.59446563	0
Rep2_TPM	28.66297559	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	699	700

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCDC124	Product_ID: A301-835A Lot_ID: 1 Source: Bethyl Labs Target Name: CCDC124-human

Experiment Status

	BGKLV32-13	BGKLV32-14
Sample_ID	BGKLV32-13	BGKLV32-14
Sample Name	CCDC124_BGKLV32-13	CCDC124_BGKLV32-14
Sample Name	CCDC124_BGKLV32-13	CCDC124_BGKLV32-14
RBP	CCDC124	CCDC124
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1161	1162

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-13	BGKLV32-14
Sample #
Sample Name	CCDC124-BGKLV32-13	CCDC124-BGKLV32-14
Sample_Name_Alias	CCDC124_BGKLV32-13	CCDC124_BGKLV32-14
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C7.png	DNA_Library_LV33-34-25B-32/set1/D7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C12.png	RNA_Library_LV29-30-31-32/set1/D12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-13	BGKLV32-14
RBP	CCDC124	CCDC124
Batch_ID	BGKLV32	BGKLV32
WB_result	63.600	63.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2846	2847

Sequencing Information

	BGKLV32-13	BGKLV32-14
Sample_ID	BGKLV32-13	BGKLV32-14
Sample Name	CCDC124_BGKLV32-13	CCDC124_BGKLV32-14
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	85,117,924	95,460,212
total_aligned_reads	72,322,418	82,420,310
unique_aligned_reads	66,231,822	75,442,562
percent_uniqueAligned	0.77812	0.79030
correlation_replicates	0.996474	0.996474
spikein_reads	319,366	368,514
percent_spikeins	0.00375	0.00386
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1495	1496

Data Submission Information

	BGKLV32-13	BGKLV32-13
ENCODE_alias	brenton-graveley:CCDC124_BGKLV32	brenton-graveley:CCDC124-BGKLV32-K562
ENCODE_accession	ENCSR874ZLI	ENCSR875BHL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-13	BGKLV32-13
Sample Name	CCDC124_BGKLV32-13	CCDC124_BGKLV32-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3120	6613

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
CCDC124_BGKLV32-13_GGCTAC_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1495	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21194
CCDC124_BGKLV32-13_GGCTAC_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1495	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21224
CCDC124_BGKLV32-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1495					GRCh38	V40	CCDC124_BGKLV32-13_GGCTAC_L002_001.R1.fastq.gz,CCDC124_BGKLV32-13_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	21254
CCDC124_BGKLV32-13_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1495					GRCh38	V40	CCDC124_BGKLV32-13/Aligned.sortedByCoord.out.bam		ENCORE2	21284
CCDC124_BGKLV32-13_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1495					GRCh38	V40	CCDC124_BGKLV32-13/Aligned.sortedByCoord.out.bam		ENCORE2	21314
CCDC124_BGKLV32-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1495					GRCh38	V40	CCDC124_BGKLV32-13/Aligned.sortedByCoord.out.bam		ENCORE2	21344
CCDC124_BGKLV32-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1495					GRCh38	V40	CCDC124_BGKLV32-13/Aligned.sortedByCoord.out.bam		ENCORE2	21374
CCDC124_BGKLV32-13_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1495					GRCh38	V40	CCDC124_BGKLV32-13_GGCTAC_L002_001.R1.fastq.gz,CCDC124_BGKLV32-13_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	21404
CCDC124_BGKLV32-14_CTTGTA_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1496	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21195
CCDC124_BGKLV32-14_CTTGTA_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1496	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21225
CCDC124_BGKLV32-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1496					GRCh38	V40	CCDC124_BGKLV32-14_CTTGTA_L002_001.R1.fastq.gz,CCDC124_BGKLV32-14_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	21255
CCDC124_BGKLV32-14_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1496					GRCh38	V40	CCDC124_BGKLV32-14/Aligned.sortedByCoord.out.bam		ENCORE2	21285
CCDC124_BGKLV32-14_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1496					GRCh38	V40	CCDC124_BGKLV32-14/Aligned.sortedByCoord.out.bam		ENCORE2	21315
CCDC124_BGKLV32-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1496					GRCh38	V40	CCDC124_BGKLV32-14/Aligned.sortedByCoord.out.bam		ENCORE2	21345
CCDC124_BGKLV32-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1496					GRCh38	V40	CCDC124_BGKLV32-14/Aligned.sortedByCoord.out.bam		ENCORE2	21375
CCDC124_BGKLV32-14_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1496					GRCh38	V40	CCDC124_BGKLV32-14_CTTGTA_L002_001.R1.fastq.gz,CCDC124_BGKLV32-14_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	21405