CDV3 RNA-Seq in K562

General Information


RBP	CDV3
Cell_Line	K562
Method	CRISPR
Exp_Name	CDV3-BGKcLV28-K562
ENCODE_series_ID	ENCSR682PUE
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR944PAO
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CDV3-BGKcLV28-15
Rep2	CDV3-BGKcLV28-16
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	82.8
Rep2_qPCR	82.0
Rep1_WB	50.7
Rep2_WB	53.9
Antibody Cat#	A304-660A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB772KPZ
Status	Released
Project	ENCODE4
ID	824

Experiment Information (Status: Released)

	BGKcLV28-15	BGKcLV28-16
idx	949	950
TRCN#_or_BGC#	BGC#0000691	BGC#0000691
shRNA_or_gRNA_sequence	CCAGAACCAGCGATGACTAG	CCAGAACCAGCGATGACTAG
PAM	TGG	TGG
Name	CDV3_92	CDV3_92
Sample_ID	BGKcLV28-15	BGKcLV28-16
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CDV3	CDV3
qPCR_result	82.8	82.0
Ave_qPCR	82.4
RT-qPCR_primer-F	agcacctcctgctccagtaa
RT-qPCR_primer-R	atttctggtggtccttgtgg
protein_conc	2171	1981
WB_result	50.7	53.9
Ave_WB	52.3
WB_DONE_date	6/22/21	JESS
MW	27kd
IP
antibody_Cat#	A304-660A	LOT #1
Antibody DCC ID	ENCAB772KPZ	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5083	5084

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

	BGKcLV28-15	BGKcLV28-16
Sample_ID	BGKcLV28-15	BGKcLV28-16
Sample Name
Sample Name	CDV3-BGKcLV28-15	CDV3-BGKcLV28-16
RBP	CDV3	CDV3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9907	9908

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-15	BGKcLV28-16
Sample #	15	16
Sample Name	CDV3-BGKcLV28-15	CDV3-BGKcLV28-16
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	366	342
Peak_Molarity	93.30	97.50
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G2.png	DNA_Library_set48-49/set3/H2.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set48-49/set2/G2.png	RNA_Library_set48-49/set2/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-15	BGKcLV28-16
RBP	CDV3	CDV3
Batch_ID	BGKcLV28	BGKcLV28
WB_result	50.700	53.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2076	2077

Sequencing Information

	BGKcLV28-15	BGKcLV28-16
Sample_ID	BGKcLV28-15	BGKcLV28-16
Sample Name	CDV3-BGKcLV28-15	CDV3-BGKcLV28-16
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	84,945,948	62,329,962
total_aligned_reads	81,037,238	59,164,676
unique_aligned_reads	74,545,658	54,373,008
percent_uniqueAligned	0.87757	0.87234
correlation_replicates	0.993059	0.993059
spikein_reads	19,646	10,270
percent_spikeins	0.00023	0.00016
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1827	1828

Data Submission Information

	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-16	BGKcLV28-16	BGKcLV28-16	BGKcLV28-16
ENCODE_alias	brenton-graveley:CDV3-BGKcLV28	brenton-graveley:CDV3-BGKcLV28-15	brenton-graveley:L-CDV3-BGKcLV28-15	brenton-graveley:CDV3-BGKcLV28-15_S97_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDV3-BGKcLV28-15_S97_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDV3-BGKcLV28-K562	brenton-graveley:CDV3-BGKcLV28-16	brenton-graveley:L-CDV3-BGKcLV28-16	brenton-graveley:CDV3-BGKcLV28-16_S98_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDV3-BGKcLV28-16_S98_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR944PAO	ENCBS154EVT	ENCLB218ROW	ENCFF604LNT	ENCFF782AFZ	ENCSR682PUE	ENCBS910GVI	ENCLB494JEG	ENCFF585FGG	ENCFF951ISR
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	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-15	BGKcLV28-16	BGKcLV28-16	BGKcLV28-16	BGKcLV28-16
Sample Name	CDV3-BGKcLV28-15	CDV3-BGKcLV28-15	CDV3-BGKcLV28-15	CDV3-BGKcLV28-15	CDV3-BGKcLV28-15	CDV3-BGKcLV28-15	CDV3-BGKcLV28-16	CDV3-BGKcLV28-16	CDV3-BGKcLV28-16	CDV3-BGKcLV28-16
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CDV3-BGKcLV28-15.pdf	L-CDV3-BGKcLV28-15.pdf				CDV3-BGKcLV28-16.pdf	L-CDV3-BGKcLV28-16.pdf
ID	3478	3590	3724	3858	3992	7131	3591	3725	3859	3993

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-BGKcLV28-15_S97_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1827	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3944
CDV3-BGKcLV28-15_S97_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1827	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4002
CDV3-BGKcLV28-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1827					GRCh38	V40	CDV3-BGKcLV28-15_S97_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGKcLV28-15_S97_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19226
CDV3-BGKcLV28-15_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1827					GRCh38	V40	CDV3-BGKcLV28-15/Aligned.sortedByCoord.out.bam		ENCORE2	19284
CDV3-BGKcLV28-15_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1827					GRCh38	V40	CDV3-BGKcLV28-15/Aligned.sortedByCoord.out.bam		ENCORE2	19342
CDV3-BGKcLV28-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1827					GRCh38	V40	CDV3-BGKcLV28-15/Aligned.sortedByCoord.out.bam		ENCORE2	19400
CDV3-BGKcLV28-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1827					GRCh38	V40	CDV3-BGKcLV28-15/Aligned.sortedByCoord.out.bam		ENCORE2	19458
CDV3-BGKcLV28-15_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1827					GRCh38	V40	CDV3-BGKcLV28-15_S97_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGKcLV28-15_S97_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19516
CDV3-BGKcLV28-16_S98_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1828	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3945
CDV3-BGKcLV28-16_S98_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1828	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4003
CDV3-BGKcLV28-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1828					GRCh38	V40	CDV3-BGKcLV28-16_S98_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGKcLV28-16_S98_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19227
CDV3-BGKcLV28-16_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1828					GRCh38	V40	CDV3-BGKcLV28-16/Aligned.sortedByCoord.out.bam		ENCORE2	19285
CDV3-BGKcLV28-16_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1828					GRCh38	V40	CDV3-BGKcLV28-16/Aligned.sortedByCoord.out.bam		ENCORE2	19343
CDV3-BGKcLV28-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1828					GRCh38	V40	CDV3-BGKcLV28-16/Aligned.sortedByCoord.out.bam		ENCORE2	19401
CDV3-BGKcLV28-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1828					GRCh38	V40	CDV3-BGKcLV28-16/Aligned.sortedByCoord.out.bam		ENCORE2	19459
CDV3-BGKcLV28-16_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1828					GRCh38	V40	CDV3-BGKcLV28-16_S98_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDV3-BGKcLV28-16_S98_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19517