CCDC47 RNA-Seq in K562

General Information


RBP	CCDC47
Cell_Line	K562
Method	CRISPR
Exp_Name	CCDC47-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CCDC47-BGKcLV35-9
Rep2	CCDC47-BGKcLV35-10
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	29.6
Rep2_qPCR	39.7
Rep1_WB	50.6
Rep2_WB	58.7
Antibody Cat#	A305-100A
Antibody Lot#	LOT# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	953

Experiment Information (Status: Submitting)

	BGKcLV35-9	BGKcLV35-10
idx	1286	1287
TRCN#_or_BGC#	BGC#0000671	BGC#0000671
shRNA_or_gRNA_sequence	AGCAGCACAGTCTCGGCGGG	AGCAGCACAGTCTCGGCGGG
PAM	AGG	AGG
Name	CCDC47_88/LAST EXON	CCDC47_88/LAST EXON
Sample_ID	BGKcLV35-9	BGKcLV35-10
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	CCDC47	CCDC47
qPCR_result	29.6	39.7
Ave_qPCR	34.7
RT-qPCR_primer-F	tacccctgatgaacatggtg
RT-qPCR_primer-R	ctactcgggcacggttctta
protein_conc	3610	2912
WB_result	49.9	52.603
Ave_WB	51.3
WB_DONE_date	6/2/22
MW	56kDa
IP	Rabbit / I
antibody_Cat#	A305-100A	LOT# 1
Antibody DCC ID	ENCAB491CRC	12/5/24
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5430	5431

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCDC47	Product_ID: A305-100A Lot_ID: 1 Source: Bethyl Labs Target Name: CCDC47-human

Experiment Status

	BGKcLV35-9	BGKcLV35-10
Sample_ID	BGKcLV35-9	BGKcLV35-10
Sample Name
Sample Name	CCDC47-BGKcLV35-9	CCDC47-BGKcLV35-10
RBP	CCDC47	CCDC47
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10863	10864

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-9	BGKcLV35-10
Sample #	29	30
Sample Name	CCDC47-BGKcLV35-9	CCDC47-BGKcLV35-10
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	282	292
Peak_Molarity	34.50	13.40
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/E8.png	DNA_Library_set54-56/set3/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/E4.png	RNA_Library_set54-56/set2/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-9	BGKcLV35-10
RBP	CCDC47	CCDC47
Batch_ID	BGKcLV35	BGKcLV35
WB_result	50.600	58.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3346	3347

Sequencing Information

	BGKcLV35-9	BGKcLV35-10
Sample_ID	BGKcLV35-9	BGKcLV35-10
Sample Name	CCDC47-BGKcLV35-9	CCDC47-BGKcLV35-10
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	75,222,240	52,451,504
total_aligned_reads	68,885,922	47,362,828
unique_aligned_reads	63,052,080	43,398,884
percent_uniqueAligned	0.83821	0.82741
correlation_replicates	0.983603	0.983603
spikein_reads	3,634	4,296
percent_spikeins	0.00005	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2225	2226

Data Submission Information DCC submission information was not avaliable

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
CCDC47-BGKcLV35-9_S31_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2225	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8483
CCDC47-BGKcLV35-9_S31_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2225	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8533
CCDC47-BGKcLV35-9_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2225					GRCh38	V40	CCDC47-BGKcLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	17729
CCDC47-BGKcLV35-9_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2225					GRCh38	V40	CCDC47-BGKcLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	17779
CCDC47-BGKcLV35-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2225					GRCh38	V40	CCDC47-BGKcLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	17829
CCDC47-BGKcLV35-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2225					GRCh38	V40	CCDC47-BGKcLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	17879
CCDC47-BGKcLV35-9_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2225					GRCh38	V40	CCDC47-BGKcLV35-9_S31_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGKcLV35-9_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17929
CCDC47-BGKcLV35-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2225					GRCh38	V40	CCDC47-BGKcLV35-9_S31_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGKcLV35-9_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29270
CCDC47-BGKcLV35-10_S32_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2226	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8482
CCDC47-BGKcLV35-10_S32_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2226	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8532
CCDC47-BGKcLV35-10_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2226					GRCh38	V40	CCDC47-BGKcLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	17728
CCDC47-BGKcLV35-10_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2226					GRCh38	V40	CCDC47-BGKcLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	17778
CCDC47-BGKcLV35-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2226					GRCh38	V40	CCDC47-BGKcLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	17828
CCDC47-BGKcLV35-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2226					GRCh38	V40	CCDC47-BGKcLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	17878
CCDC47-BGKcLV35-10_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2226					GRCh38	V40	CCDC47-BGKcLV35-10_S32_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGKcLV35-10_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17928
CCDC47-BGKcLV35-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2226					GRCh38	V40	CCDC47-BGKcLV35-10_S32_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGKcLV35-10_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29269