WRN RNA-Seq in HepG2

General Information


RBP	WRN
Cell_Line	HepG2
Method	shRNA
Exp_Name	WRN-BGHLV37-HepG2
ENCODE_series_ID	ENCSR115JEY
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR093FHC
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	WRN-BGHLV37-87C
Rep2	WRN-BGHLV37-88C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	33.5
Rep2_qPCR	21.2
Rep1_WB	98.1
Rep2_WB	89.6
Antibody Cat#	GTX101081
Antibody Lot#	GTX101081
Antibody DCC ID	ENCAB362RRM
Status	Released
Project	ENCODE4
ID	265

Experiment Information (Status: Released)

	BGHLV37-87	BGHLV37-88
idx	999	1000
TRCN#_or_BGC#	TRCN0000004901	TRCN0000004901
shRNA_or_gRNA_sequence	CCATTATACAATAGAGGGAAA	CCATTATACAATAGAGGGAAA
PAM
Name	WRN	WRN
Sample_ID	BGHLV37-87	BGHLV37-88
transduction_Date	9/1/16	9/1/16
days
RBP_name	WRN	WRN
qPCR_result	33.5	21.2
Ave_qPCR	27.4
RT-qPCR_primer-F	TTCAAGTTCTAAGAGAAGCAAGGAA
RT-qPCR_primer-R	TTGGCAAACCACACAGGTAA
protein_conc	4156	3819
WB_result	98.1	89.6
Ave_WB	93.9
WB_DONE_date	9/20/16	WES
MW	162kd
IP	1IP	1IP
antibody_Cat#	GTX101081	GTX101081
Antibody DCC ID	ENCAB362RRM	ENCAB362RRM
submitted_to_DCC_date	10/26/16
Rep1_TPM	11.4	0
Rep2_TPM	9.3	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3092	3093

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WRN	Product_ID: GTX101081 Lot_ID: 39812 Source: GeneTex Target Name: WRN-human

Experiment Status

	BGHLV37-87	BGHLV37-88
Sample_ID	BGHLV37-87	BGHLV37-88
Sample Name
Sample Name	WRN-BGHLV37-87C	WRN-BGHLV37-88C
RBP	WRN	WRN
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6441	6442

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-87	BGHLV37-88
Sample #	25	26
Sample Name	WRN-BGHLV37-87C	WRN-BGHLV37-88C
Sample_Name_Alias
Index Well Position	S11	S12
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	302	307
Peak_Molarity	20.30	28.60
libSampleQC_DNA_Well	DNA_Library_set40/set1/C6.png	DNA_Library_set40/set1/D6.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set40/set1/A2.png	RNA_Library_set40/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-87	BGHLV37-88
RBP	WRN	WRN
Batch_ID	BGHLV37	BGHLV37
WB_result	98.100	89.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	948	949

Sequencing Information

	BGHLV37-87	BGHLV37-88
Sample_ID	BGHLV37-87	BGHLV37-88
Sample Name	WRN-BGHLV37-87C	WRN-BGHLV37-88C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	35,955,026	29,650,046
total_aligned_reads	30,741,300	24,604,608
unique_aligned_reads	28,900,104	23,136,402
percent_uniqueAligned	0.80378	0.78032
correlation_replicates	0.995003	0.995003
spikein_reads	9,636	7,084
percent_spikeins	0.00027	0.00024
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	351	352

Data Submission Information

	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-88	BGHLV37-88	BGHLV37-88	BGHLV37-88
ENCODE_alias	brenton-graveley:WRN-BGHLV37-C	brenton-graveley:WRN-BGHLV37-87C	brenton-graveley:L-WRN-BGHLV37-87C	brenton-graveley:WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R2.fastq.gz	brenton-graveley:WRN-BGHLV37-HepG2	brenton-graveley:WRN-BGHLV37-88C	brenton-graveley:L-WRN-BGHLV37-88C	brenton-graveley:WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR093FHC	ENCBS209JZM	ENCLB652SCH	ENCFF656UDL	ENCFF552JWT	ENCSR115JEY	ENCBS466LQV	ENCLB861KBS	ENCFF491QIV	ENCFF363UDM
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	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-87	BGHLV37-88	BGHLV37-88	BGHLV37-88	BGHLV37-88
Sample Name	WRN-BGHLV37-87C	WRN-BGHLV37-87C	WRN-BGHLV37-87C	WRN-BGHLV37-87C	WRN-BGHLV37-87C	WRN-BGHLV37-87C	WRN-BGHLV37-88C	WRN-BGHLV37-88C	WRN-BGHLV37-88C	WRN-BGHLV37-88C
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		WRN-BGHLV37-87C.pdf	L-WRN-BGHLV37-87C.pdf				WRN-BGHLV37-88C.pdf	L-WRN-BGHLV37-88C.pdf
ID	1451	1500	1556	1595	1632	7353	1501	1557	1596	1633

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
WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	351	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	665
WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	351	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	707
WRN-BGHLV37-87C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	351					GRCh38	V40	WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R1.fastq.gz,WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23268
WRN-BGHLV37-87C_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	351					GRCh38	V40	WRN-BGHLV37-87C/Aligned.sortedByCoord.out.bam		ENCORE2	23302
WRN-BGHLV37-87C_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	351					GRCh38	V40	WRN-BGHLV37-87C/Aligned.sortedByCoord.out.bam		ENCORE2	23336
WRN-BGHLV37-87C_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	351					GRCh38	V40	WRN-BGHLV37-87C/Aligned.sortedByCoord.out.bam		ENCORE2	23370
WRN-BGHLV37-87C_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	351					GRCh38	V40	WRN-BGHLV37-87C/Aligned.sortedByCoord.out.bam		ENCORE2	23404
WRN-BGHLV37-87C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	351					GRCh38	V40	WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R1.fastq.gz,WRN-BGHLV37-87C_GGCTAC_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23438
WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	352	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	666
WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	352	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	708
WRN-BGHLV37-88C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	352					GRCh38	V40	WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R1.fastq.gz,WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23269
WRN-BGHLV37-88C_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	352					GRCh38	V40	WRN-BGHLV37-88C/Aligned.sortedByCoord.out.bam		ENCORE2	23303
WRN-BGHLV37-88C_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	352					GRCh38	V40	WRN-BGHLV37-88C/Aligned.sortedByCoord.out.bam		ENCORE2	23337
WRN-BGHLV37-88C_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	352					GRCh38	V40	WRN-BGHLV37-88C/Aligned.sortedByCoord.out.bam		ENCORE2	23371
WRN-BGHLV37-88C_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	352					GRCh38	V40	WRN-BGHLV37-88C/Aligned.sortedByCoord.out.bam		ENCORE2	23405
WRN-BGHLV37-88C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	352					GRCh38	V40	WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R1.fastq.gz,WRN-BGHLV37-88C_CTTGTA_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23439