WDR43 RNA-Seq in HepG2

General Information


RBP	WDR43
Cell_Line	HepG2
Method	CRISPR
Exp_Name	WDR43-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR952JNE
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR606QVN
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	WDR43-BGHcLV12-87
Rep2	WDR43-BGHcLV12-88
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	71.9
Rep2_WB	68.1
Antibody Cat#	A302-478A
Antibody Lot#
Antibody DCC ID	ENCAB350LKS
Status	Released
Project	ENCODE4
ID	195

Experiment Information (Status: Released)

	BGHcLV12-87	BGHcLV12-88
idx	347	348
TRCN#_or_BGC#	BGC#0000297	BGC#0000297
shRNA_or_gRNA_sequence	CCGACGGTCACTTACGAGTA	CCGACGGTCACTTACGAGTA
PAM	tgg	tgg
Name	WDR43_99	WDR43_99
Sample_ID	BGHcLV12-87	BGHcLV12-88
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	WDR43	WDR43
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5812	5827
WB_result	71.9	68.1
Ave_WB	70.0	no specific band stroger then specific
WB_DONE_date	2/4/19
MW	75kda
IP
antibody_Cat#	A302-478A
Antibody DCC ID	ENCAB350LKS
submitted_to_DCC_date	2/22/19
Rep1_TPM	56	0
Rep2_TPM	49	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6492	6493

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WDR43	Product_ID: A302-478A Lot_ID: 1 Source: Bethyl Labs Target Name: WDR43-human

Experiment Status

	BGHcLV12-87	BGHcLV12-88
Sample_ID	BGHcLV12-87	BGHcLV12-88
Sample Name	WDR43-BGHcLV12-87	WDR43-BGHcLV12-88
Sample Name	WDR43-BGHcLV12-87	WDR43-BGHcLV12-88
RBP	WDR43	WDR43
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2817	2818

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-87	BGHcLV12-88
Sample #	47	48
Sample Name	WDR43-BGHcLV12-87	WDR43-BGHcLV12-88
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-G2	3-H2
Tecan	43.04	37.29
Tecan_date	2019-03-13	2019-03-13
Size_bp	309	295
Peak_Molarity	68.80	38.90
libSampleQC_DNA_Well	DNA_Library_set42/set1/G6.png	DNA_Library_set42/set1/H6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set42/set1/G6.png	RNA_Library_set42/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-87	BGHcLV12-88
RBP	WDR43	WDR43
Batch_ID	BGHcLV12	BGHcLV12
WB_result	71.900	68.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	47	48

Sequencing Information

	BGHcLV12-87	BGHcLV12-88
Sample_ID	BGHcLV12-87	BGHcLV12-88
Sample Name	WDR43-BGHcLV12-87	WDR43-BGHcLV12-88
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	165,666,386	58,024,060
total_aligned_reads	157,937,730	56,015,578
unique_aligned_reads	148,070,202	52,718,132
percent_uniqueAligned	0.89379	0.90856
correlation_replicates	0.996817	0.996817
spikein_reads	93,194	53,358
percent_spikeins	0.00056	0.00092
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	77	78

Data Submission Information

	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-88	BGHcLV12-88	BGHcLV12-88	BGHcLV12-88
ENCODE_alias	brenton-graveley:WDR43-BGHcLV12	brenton-graveley:WDR43-BGHcLV12-87	brenton-graveley:L-WDR43-BGHcLV12-87	brenton-graveley:WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WDR43-BGHcLV12-HepG2	brenton-graveley:WDR43-BGHcLV12-88	brenton-graveley:L-WDR43-BGHcLV12-88	brenton-graveley:WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR606QVN	ENCBS260ZXT	ENCLB687ZQU	ENCFF809QTD	ENCFF719KZI	ENCSR952JNE	ENCBS795OMT	ENCLB717VDA	ENCFF932OGK	ENCFF851CGS
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	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-87	BGHcLV12-88	BGHcLV12-88	BGHcLV12-88	BGHcLV12-88
Sample Name	WDR43-BGHcLV12-87	WDR43-BGHcLV12-87	WDR43-BGHcLV12-87	WDR43-BGHcLV12-87	WDR43-BGHcLV12-87	WDR43-BGHcLV12-87	WDR43-BGHcLV12-88	WDR43-BGHcLV12-88	WDR43-BGHcLV12-88	WDR43-BGHcLV12-88
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		WDR43-BGHcLV12-87.pdf	L-WDR43-BGHcLV12-87.pdf				WDR43-BGHcLV12-88.pdf	L-WDR43-BGHcLV12-88.pdf
ID	754	803	885	1027	1109	7352	804	886	1028	1110

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
WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	77	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	409
WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	77	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	491
WDR43-BGHcLV12-87_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	77					GRCh38	V40	WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz,WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23748
WDR43-BGHcLV12-87_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	77					GRCh38	V40	WDR43-BGHcLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	23830
WDR43-BGHcLV12-87_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	77					GRCh38	V40	WDR43-BGHcLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	23912
WDR43-BGHcLV12-87_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	77					GRCh38	V40	WDR43-BGHcLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	23994
WDR43-BGHcLV12-87_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	77					GRCh38	V40	WDR43-BGHcLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	24076
WDR43-BGHcLV12-87_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	77					GRCh38	V40	WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz,WDR43-BGHcLV12-87_GTTCCAAT+AATTCTGC_HK3H2DSXX_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24158
WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	78	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	410
WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	78	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	492
WDR43-BGHcLV12-88_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	78					GRCh38	V40	WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz,WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23749
WDR43-BGHcLV12-88_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	78					GRCh38	V40	WDR43-BGHcLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	23831
WDR43-BGHcLV12-88_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	78					GRCh38	V40	WDR43-BGHcLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	23913
WDR43-BGHcLV12-88_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	78					GRCh38	V40	WDR43-BGHcLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	23995
WDR43-BGHcLV12-88_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	78					GRCh38	V40	WDR43-BGHcLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	24077
WDR43-BGHcLV12-88_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	78					GRCh38	V40	WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz,WDR43-BGHcLV12-88_ACCTTGGC+GGCCTCAT_HK3H2DSXX_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24159