CCDC47 RNA-Seq in HepG2

General Information


RBP	CCDC47
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CCDC47-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR911GHJ
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR583SHC
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	CCDC47-BGHcLV27-45
Rep2	CCDC47-BGHcLV27-46
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	69.3
Rep2_qPCR	74.3
Rep1_WB	81.1
Rep2_WB	66.9
Antibody Cat#	A305-100A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB491CRC
Status	Released
Project	ENCODE4
ID	817

Experiment Information (Status: Released)

	BGHcLV27-45	BGHcLV27-45	BGHcLV27-46	BGHcLV27-46
idx	811	811	812	812
TRCN#_or_BGC#	BGC#0000672	BGC#0000672	BGC#0000672	BGC#0000672
shRNA_or_gRNA_sequence	GGCCTGGTTTAACACTCATA	GGCCTGGTTTAACACTCATA	GGCCTGGTTTAACACTCATA	GGCCTGGTTTAACACTCATA
PAM	GGG	GGG	GGG	GGG
Name	CCDC47_90	CCDC47_90	CCDC47_90	CCDC47_90
Sample_ID	BGHcLV27-45	BGHcLV27-45	BGHcLV27-46	BGHcLV27-46
transduction_Date	5/18/21	5/18/21	5/18/21	5/18/21
days	D6	D6	D6	D6
RBP_name	CCDC47	CCDC47	CCDC47	CCDC47
qPCR_result	69.3	69.3	74.3	74.3
Ave_qPCR	71.8	71.8
RT-qPCR_primer-F	tacccctgatgaacatggtg	tacccctgatgaacatggtg
RT-qPCR_primer-R	ctactcgggcacggttctta	ctactcgggcacggttctta
protein_conc	3539	3539	4037	4037
WB_result	69.9	not as good as A304-970A, more non-sepcific bands	62.3
Ave_WB	66.1
WB_DONE_date	11/4/21	4/18/22
MW	56kDa	56kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A305-100A	A305-101A	LOT# 1	LOT# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/03/21		09/03/21
repeat_library
Note
ID	6980	6982	6981	6983

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV27-45	BGHcLV27-46
Sample_ID	BGHcLV27-45	BGHcLV27-46
Sample Name
Sample Name	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-46
RBP	CCDC47	CCDC47
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9697	9698

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-45	BGHcLV27-46
Sample #	101	102
Sample Name	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-46
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	291	292
Peak_Molarity	147.00	153.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/A10.png	DNA_Library_set48-49/set2/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set48-49/set1/C10.png	RNA_Library_set48-49/set1/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-45	BGHcLV27-46
RBP	CCDC47	CCDC47
Batch_ID	BGHcLV27	BGHcLV27
WB_result	81.100	66.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1660	1661

Sequencing Information

	BGHcLV27-45	BGHcLV27-46
Sample_ID	BGHcLV27-45	BGHcLV27-46
Sample Name	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-46
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	61,391,606	58,306,550
total_aligned_reads	54,533,110	51,359,356
unique_aligned_reads	51,336,064	48,300,752
percent_uniqueAligned	0.83621	0.82839
correlation_replicates	0.996889	0.996889
spikein_reads	20,604	13,792
percent_spikeins	0.00034	0.00024
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1811	1812

Data Submission Information

	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-46	BGHcLV27-46	BGHcLV27-46	BGHcLV27-46
ENCODE_alias	brenton-graveley:CCDC47-BGHcLV27	brenton-graveley:CCDC47-BGHcLV27-45	brenton-graveley:L-CCDC47-BGHcLV27-45	brenton-graveley:CCDC47-BGHcLV27-45_S81_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCDC47-BGHcLV27-45_S81_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCDC47-BGHcLV27-HepG2	brenton-graveley:CCDC47-BGHcLV27-46	brenton-graveley:L-CCDC47-BGHcLV27-46	brenton-graveley:CCDC47-BGHcLV27-46_S82_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCDC47-BGHcLV27-46_S82_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR583SHC	ENCBS775FFI	ENCLB281QYA	ENCFF149VCA	ENCFF204PNZ	ENCSR911GHJ	ENCBS636MAC	ENCLB232RAK	ENCFF705KAQ	ENCFF472GGX
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
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	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-45	BGHcLV27-46	BGHcLV27-46	BGHcLV27-46	BGHcLV27-46
Sample Name	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-45	CCDC47-BGHcLV27-46	CCDC47-BGHcLV27-46	CCDC47-BGHcLV27-46	CCDC47-BGHcLV27-46
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV48H_library_protocol					LV48H_library_protocol
protocol_URL			L-CCDC47-BGHcLV27-45.pdf					L-CCDC47-BGHcLV27-46.pdf
ID	3445	3524	3658	3792	3926	7120	3525	3659	3793	3927

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-BGHcLV27-45_S81_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1811	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3802
CCDC47-BGHcLV27-45_S81_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1811	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3828
CCDC47-BGHcLV27-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1811					GRCh38	V40	CCDC47-BGHcLV27-45_S81_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGHcLV27-45_S81_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25489
CCDC47-BGHcLV27-45_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1811					GRCh38	V40	CCDC47-BGHcLV27-45_S81_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGHcLV27-45_S81_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25515
CCDC47-BGHcLV27-45_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1811					GRCh38	V40	CCDC47-BGHcLV27-45/Aligned.sortedByCoord.out.bam		ENCORE2	26453
CCDC47-BGHcLV27-45_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1811					GRCh38	V40	CCDC47-BGHcLV27-45/Aligned.sortedByCoord.out.bam		ENCORE2	26479
CCDC47-BGHcLV27-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1811					GRCh38	V40	CCDC47-BGHcLV27-45/Aligned.sortedByCoord.out.bam		ENCORE2	26505
CCDC47-BGHcLV27-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1811					GRCh38	V40	CCDC47-BGHcLV27-45/Aligned.sortedByCoord.out.bam		ENCORE2	26531
CCDC47-BGHcLV27-46_S82_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1812	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3803
CCDC47-BGHcLV27-46_S82_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1812	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3829
CCDC47-BGHcLV27-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1812					GRCh38	V40	CCDC47-BGHcLV27-46_S82_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGHcLV27-46_S82_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25490
CCDC47-BGHcLV27-46_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1812					GRCh38	V40	CCDC47-BGHcLV27-46_S82_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCDC47-BGHcLV27-46_S82_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25516
CCDC47-BGHcLV27-46_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1812					GRCh38	V40	CCDC47-BGHcLV27-46/Aligned.sortedByCoord.out.bam		ENCORE2	26454
CCDC47-BGHcLV27-46_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1812					GRCh38	V40	CCDC47-BGHcLV27-46/Aligned.sortedByCoord.out.bam		ENCORE2	26480
CCDC47-BGHcLV27-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1812					GRCh38	V40	CCDC47-BGHcLV27-46/Aligned.sortedByCoord.out.bam		ENCORE2	26506
CCDC47-BGHcLV27-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1812					GRCh38	V40	CCDC47-BGHcLV27-46/Aligned.sortedByCoord.out.bam		ENCORE2	26532