WDR3 RNA-Seq in HepG2

General Information


RBP	WDR3
Cell_Line	HepG2
Method	shRNA
Exp_Name	WDR3-BGHLV37-HepG2
ENCODE_series_ID	ENCSR398UWJ
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR902VPO
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	WDR3-BGHLV37-75C
Rep2	WDR3-BGHLV37-76C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	59.2
Rep2_qPCR	63.5
Rep1_WB	81.7
Rep2_WB	79.5
Antibody Cat#	A301-553A
Antibody Lot#	A301-553A
Antibody DCC ID	ENCAB768ADR
Status	Released
Project	ENCODE4
ID	264

Experiment Information (Status: Released)

	BGHLV37-75	BGHLV37-76
idx	987	988
TRCN#_or_BGC#	TRCN0000128408	TRCN0000128408
shRNA_or_gRNA_sequence	GTGCATAATTGATTGCCCTTT	GTGCATAATTGATTGCCCTTT
PAM
Name	WDR3	WDR3
Sample_ID	BGHLV37-75	BGHLV37-76
transduction_Date	9/1/16	9/1/16
days
RBP_name	WDR3	WDR3
qPCR_result	59.2	63.5
Ave_qPCR	61.4
RT-qPCR_primer-F	acaaggatgccatcacacaa
RT-qPCR_primer-R	atcaaggtcccaccatttca
protein_conc	4946	4394
WB_result	81.7	79.5
Ave_WB	80.6
WB_DONE_date	9/20/16	WES
MW	106kDa
IP	1	1
antibody_Cat#	A301-553A	A301-553A
Antibody DCC ID	ENCAB768ADR	ENCAB768ADR
submitted_to_DCC_date	10/26/16
Rep1_TPM	13.3	0
Rep2_TPM	12.4	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3080	3081

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WDR3	Product_ID: A301-553A Lot_ID: 1 Source: Bethyl Labs Target Name: WDR3-human

Experiment Status

	BGHLV37-75	BGHLV37-76
Sample_ID	BGHLV37-75	BGHLV37-76
Sample Name
Sample Name	WDR3-BGHLV37-75C	WDR3-BGHLV37-76C
RBP	WDR3	WDR3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6439	6440

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-75	BGHLV37-76
Sample #	23	24
Sample Name	WDR3-BGHLV37-75C	WDR3-BGHLV37-76C
Sample_Name_Alias
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	308	338
Peak_Molarity	22.70	28.90
libSampleQC_DNA_Well	DNA_Library_set40/set1/A6.png	DNA_Library_set40/set1/B6.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set40/set1/G1.png	RNA_Library_set40/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-75	BGHLV37-76
RBP	WDR3	WDR3
Batch_ID	BGHLV37	BGHLV37
WB_result	81.700	79.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	946	947

Sequencing Information

	BGHLV37-75	BGHLV37-76
Sample_ID	BGHLV37-75	BGHLV37-76
Sample Name	WDR3-BGHLV37-75C	WDR3-BGHLV37-76C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	49,748,722	32,749,698
total_aligned_reads	42,235,220	28,545,816
unique_aligned_reads	39,855,038	26,976,370
percent_uniqueAligned	0.80113	0.82371
correlation_replicates	0.996669	0.996669
spikein_reads	18,224	22,052
percent_spikeins	0.00037	0.00067
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	349	350

Data Submission Information

	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-76	BGHLV37-76	BGHLV37-76	BGHLV37-76
ENCODE_alias	brenton-graveley:WDR3-BGHLV37-C	brenton-graveley:WDR3-BGHLV37-75C	brenton-graveley:L-WDR3-BGHLV37-75C	brenton-graveley:WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R2.fastq.gz	brenton-graveley:WDR3-BGHLV37-HepG2	brenton-graveley:WDR3-BGHLV37-76C	brenton-graveley:L-WDR3-BGHLV37-76C	brenton-graveley:WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR902VPO	ENCBS952ZRG	ENCLB512JKW	ENCFF358KYL	ENCFF638UWY	ENCSR398UWJ	ENCBS286UBI	ENCLB321UHL	ENCFF558HRO	ENCFF184PIP
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	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-75	BGHLV37-76	BGHLV37-76	BGHLV37-76	BGHLV37-76
Sample Name	WDR3-BGHLV37-75C	WDR3-BGHLV37-75C	WDR3-BGHLV37-75C	WDR3-BGHLV37-75C	WDR3-BGHLV37-75C	WDR3-BGHLV37-75C	WDR3-BGHLV37-76C	WDR3-BGHLV37-76C	WDR3-BGHLV37-76C	WDR3-BGHLV37-76C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		WDR3-BGHLV37-75C.pdf	L-WDR3-BGHLV37-75C.pdf				WDR3-BGHLV37-76C.pdf	L-WDR3-BGHLV37-76C.pdf
ID	1450	1498	1554	1593	1630	7351	1499	1555	1594	1631

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
WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	349	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	663
WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	349	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	705
WDR3-BGHLV37-75C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	349					GRCh38	V40	WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R1.fastq.gz,WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23266
WDR3-BGHLV37-75C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	349					GRCh38	V40	WDR3-BGHLV37-75C/Aligned.sortedByCoord.out.bam		ENCORE2	23300
WDR3-BGHLV37-75C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	349					GRCh38	V40	WDR3-BGHLV37-75C/Aligned.sortedByCoord.out.bam		ENCORE2	23334
WDR3-BGHLV37-75C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	349					GRCh38	V40	WDR3-BGHLV37-75C/Aligned.sortedByCoord.out.bam		ENCORE2	23368
WDR3-BGHLV37-75C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	349					GRCh38	V40	WDR3-BGHLV37-75C/Aligned.sortedByCoord.out.bam		ENCORE2	23402
WDR3-BGHLV37-75C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	349					GRCh38	V40	WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R1.fastq.gz,WDR3-BGHLV37-75C_GATCAG_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23436
WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	350	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	664
WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	350	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	706
WDR3-BGHLV37-76C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	350					GRCh38	V40	WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R1.fastq.gz,WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23267
WDR3-BGHLV37-76C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	350					GRCh38	V40	WDR3-BGHLV37-76C/Aligned.sortedByCoord.out.bam		ENCORE2	23301
WDR3-BGHLV37-76C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	350					GRCh38	V40	WDR3-BGHLV37-76C/Aligned.sortedByCoord.out.bam		ENCORE2	23335
WDR3-BGHLV37-76C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	350					GRCh38	V40	WDR3-BGHLV37-76C/Aligned.sortedByCoord.out.bam		ENCORE2	23369
WDR3-BGHLV37-76C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	350					GRCh38	V40	WDR3-BGHLV37-76C/Aligned.sortedByCoord.out.bam		ENCORE2	23403
WDR3-BGHLV37-76C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	350					GRCh38	V40	WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R1.fastq.gz,WDR3-BGHLV37-76C_TAGCTT_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23437