CDV3 RNA-Seq in HepG2

General Information


RBP	CDV3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CDV3-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR606NBL
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR875UMY
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CDV3-BGHcLV29-15
Rep2	CDV3-BGHcLV29-16
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	76.8
Rep2_qPCR	76.5
Rep1_WB	57.2
Rep2_WB	76.4
Antibody Cat#	A304-660A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB772KPZ
Status	Submitted
Project	ENCODE4
ID	849

Experiment Information (Status: Released)

	BGHcLV29-15	BGHcLV29-16
idx	846	847
TRCN#_or_BGC#	BGC#0000691	BGC#0000691
shRNA_or_gRNA_sequence	CCAGAACCAGCGATGACTAG	CCAGAACCAGCGATGACTAG
PAM	TGG	TGG
Name	CDV3_92	CDV3_92
Sample_ID	BGHcLV29-15	BGHcLV29-16
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CDV3	CDV3
qPCR_result	76.8	76.5
Ave_qPCR	76.65
RT-qPCR_primer-F	agcacctcctgctccagtaa
RT-qPCR_primer-R	atttctggtggtccttgtgg
protein_conc	0	4914
WB_result	57.2	76.4
Ave_WB	66.8
WB_DONE_date	10/8/21	JESS
MW	27kd
IP	Rabbit / I
antibody_Cat#	A304-660A	LOT #1
Antibody DCC ID	ENCAB772KPZ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7023	7024

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDV3	Product_ID: A304-660A Lot_ID: 1 Source: Bethyl Labs Target Name: CDV3-human

Experiment Status

	BGHcLV29-15	BGHcLV29-16
Sample_ID	BGHcLV29-15	BGHcLV29-16
Sample Name
Sample Name	CDV3-BGHcLV29-15	CDV3-BGHcLV29-16
RBP	CDV3	CDV3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9983	9984

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-15	BGHcLV29-16
Sample #	11	12
Sample Name	CDV3-BGHcLV29-15	CDV3-BGHcLV29-16
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	295	297
Peak_Molarity	39.80	39.10
libSampleQC_DNA_Well	DNA_Library_set50/set1/C2.png	DNA_Library_set50/set1/D2.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set1/C8.png	RNA_Library_set50/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-15	BGHcLV29-16
RBP	CDV3	CDV3
Batch_ID	BGHcLV29	BGHcLV29
WB_result	57.200	76.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3098	3099

Sequencing Information

	BGHcLV29-15	BGHcLV29-16
Sample_ID	BGHcLV29-15	BGHcLV29-16
Sample Name	CDV3-BGHcLV29-15	CDV3-BGHcLV29-16
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	60,524,546	71,623,326
total_aligned_reads	55,720,500	67,174,026
unique_aligned_reads	52,617,892	63,428,716
percent_uniqueAligned	0.86936	0.88559
correlation_replicates	0.999081	0.999081
spikein_reads	17,606	12,772
percent_spikeins	0.00029	0.00018
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1879	1880

Data Submission Information

	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-16	BGHcLV29-16	BGHcLV29-16	BGHcLV29-16
ENCODE_alias	brenton-graveley:CDV3-BGHcLV29	brenton-graveley:CDV3-BGHcLV29-15	brenton-graveley:L-CDV3-BGHcLV29-15	brenton-graveley:CDV3-BGHcLV29-15_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDV3-BGHcLV29-15_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDV3-BGHcLV29-HepG2	brenton-graveley:CDV3-BGHcLV29-16	brenton-graveley:L-CDV3-BGHcLV29-16	brenton-graveley:CDV3-BGHcLV29-16_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDV3-BGHcLV29-16_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR875UMY	ENCBS480AAL	ENCLB526WGG	ENCFF006RLD	ENCFF060JUD	ENCSR606NBL	ENCBS450LGX	ENCLB698PTQ	ENCFF208XBC	ENCFF093MPE
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	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-15	BGHcLV29-16	BGHcLV29-16	BGHcLV29-16	BGHcLV29-16
Sample Name	CDV3-BGHcLV29-15	CDV3-BGHcLV29-15	CDV3-BGHcLV29-15	CDV3-BGHcLV29-15	CDV3-BGHcLV29-15	CDV3-BGHcLV29-15	CDV3-BGHcLV29-16	CDV3-BGHcLV29-16	CDV3-BGHcLV29-16	CDV3-BGHcLV29-16
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		CDV3-BGHcLV29-15.pdf	L-CDV3-BGHcLV29-15.pdf				CDV3-BGHcLV29-16.pdf	L-CDV3-BGHcLV29-16.pdf
ID	5847	5887	5959	6031	6103	6170	5888	5960	6032	6104

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
CDV3-BGHcLV29-15_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1879	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5767
CDV3-BGHcLV29-15_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1879	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5809
CDV3-BGHcLV29-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1879					GRCh38	V40	CDV3-BGHcLV29-15_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGHcLV29-15_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18934
CDV3-BGHcLV29-15_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1879					GRCh38	V40	CDV3-BGHcLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	18992
CDV3-BGHcLV29-15_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1879					GRCh38	V40	CDV3-BGHcLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	19038
CDV3-BGHcLV29-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1879					GRCh38	V40	CDV3-BGHcLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	19084
CDV3-BGHcLV29-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1879					GRCh38	V40	CDV3-BGHcLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	19130
CDV3-BGHcLV29-15_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1879					GRCh38	V40	CDV3-BGHcLV29-15_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGHcLV29-15_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19176
CDV3-BGHcLV29-16_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1880	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5768
CDV3-BGHcLV29-16_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1880	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5810
CDV3-BGHcLV29-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1880					GRCh38	V40	CDV3-BGHcLV29-16_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGHcLV29-16_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18935
CDV3-BGHcLV29-16_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1880					GRCh38	V40	CDV3-BGHcLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	18993
CDV3-BGHcLV29-16_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1880					GRCh38	V40	CDV3-BGHcLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	19039
CDV3-BGHcLV29-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1880					GRCh38	V40	CDV3-BGHcLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	19085
CDV3-BGHcLV29-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1880					GRCh38	V40	CDV3-BGHcLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	19131
CDV3-BGHcLV29-16_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1880					GRCh38	V40	CDV3-BGHcLV29-16_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGHcLV29-16_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19177