WRN RNA-Seq in K562

General Information


RBP	WRN
Cell_Line	K562
Method	shRNA
Exp_Name	WRN-BGKLV38-K562
ENCODE_series_ID	ENCSR448OED
Batch_ID	BGKLV38
Pool ID	Pool-161129
Local_Set_Name	set38
ENCODE_KD_Exp_ID	ENCSR165BCF
ENCODE_CN_Exp_ID	ENCSR718EWL
Rep1	WRN_BGKLV38-109
Rep2	WRN_BGKLV38-110
CN1	NT_BGKLV38-1
CN2	NT_BGKLV38-2
Rep1_qPCR	48.4
Rep2_qPCR	38.2
Rep1_WB	71.2
Rep2_WB	80.4
Antibody Cat#	GTX101081
Antibody Lot#	GTX101081
Antibody DCC ID	ENCAB362RRM
Status	Released
Project	ENCODE3
ID	757

Experiment Information (Status: Released)

	BGKLV38-109	BGKLV38-110
idx	880	881
TRCN#_or_BGC#	TRCN0000004899	TRCN0000004899
shRNA_or_gRNA_sequence	CCTGTAAGATTGCTTTAAGAA	CCTGTAAGATTGCTTTAAGAA
PAM
Name	WRN	WRN
Sample_ID	BGKLV38-109	BGKLV38-110
transduction_Date	9/15/16	9/15/16
days
RBP_name	WRN	WRN
qPCR_result	48.4	38.2
Ave_qPCR	43.3
RT-qPCR_primer-F	TTCAAGTTCTAAGAGAAGCAAGGAA
RT-qPCR_primer-R	TTGGCAAACCACACAGGTAA
protein_conc	2542	2669
WB_result	71.2	80.4
Ave_WB	75.8
WB_DONE_date	10/18/16	WES
MW	162kd
IP	1IP	1IP
antibody_Cat#	GTX101081	GTX101081
Antibody DCC ID	ENCAB362RRM	ENCAB362RRM
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	977	978

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

	BGKLV38-109	BGKLV38-110
Sample_ID	BGKLV38-109	BGKLV38-110
Sample Name	WRN_BGKLV38-109	WRN_BGKLV38-110
Sample Name	WRN_BGKLV38-109	WRN_BGKLV38-110
RBP	WRN	WRN
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1311	1312

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-109	BGKLV38-110
Sample #
Sample Name	WRN-BGKLV38-109	WRN-BGKLV38-110
Sample_Name_Alias	WRN_BGKLV38-109	WRN_BGKLV38-110
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/A6.png	DNA_Library_LV37-38/set1/B6.png
RIN	9.4	9.1
libSample_RNA_Well	RNA_Library_LV37_38/set2/A1.png	RNA_Library_LV37_38/set2/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV38-109	BGKLV38-110
RBP	WRN	WRN
Batch_ID	BGKLV38	BGKLV38
WB_result	71.200	80.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3002	3003

Sequencing Information

	BGKLV38-109	BGKLV38-110
Sample_ID	BGKLV38-109	BGKLV38-110
Sample Name	WRN_BGKLV38-109	WRN_BGKLV38-110
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set38	set38
total_reads	93,655,852	106,000,000
total_aligned_reads	83,886,292	97,900,510
unique_aligned_reads	76,066,422	88,778,756
percent_uniqueAligned	0.81219	0.83754
correlation_replicates	0.996027	0.996027
spikein_reads	203,750	191,168
percent_spikeins	0.00218	0.00180
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1651	1652

Data Submission Information

	BGKLV38-109	BGKLV38-109
ENCODE_alias	brenton-graveley:WRN_BGKLV38	brenton-graveley:WRN-BGKLV38-K562
ENCODE_accession	ENCSR165BCF	ENCSR448OED
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV38-109	BGKLV38-109
Sample Name	WRN_BGKLV38-109	WRN_BGKLV38-109
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3195	7040

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_BGKLV38-109_GTCCGC_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1651	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22182
WRN_BGKLV38-109_GTCCGC_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1651	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22194
WRN_BGKLV38-109_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1651					GRCh38	V40	WRN_BGKLV38-109_GTCCGC_L008_001.R1.fastq.gz,WRN_BGKLV38-109_GTCCGC_L008_001.R2.fastq.gz		ENCORE2	22206
WRN_BGKLV38-109_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1651					GRCh38	V40	WRN_BGKLV38-109/Aligned.sortedByCoord.out.bam		ENCORE2	22218
WRN_BGKLV38-109_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1651					GRCh38	V40	WRN_BGKLV38-109/Aligned.sortedByCoord.out.bam		ENCORE2	22230
WRN_BGKLV38-109_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1651					GRCh38	V40	WRN_BGKLV38-109/Aligned.sortedByCoord.out.bam		ENCORE2	22242
WRN_BGKLV38-109_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1651					GRCh38	V40	WRN_BGKLV38-109/Aligned.sortedByCoord.out.bam		ENCORE2	22254
WRN_BGKLV38-109_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1651					GRCh38	V40	WRN_BGKLV38-109_GTCCGC_L008_001.R1.fastq.gz,WRN_BGKLV38-109_GTCCGC_L008_001.R2.fastq.gz		ENCORE2	22266
WRN_BGKLV38-110_GTGAAA_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1652	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22183
WRN_BGKLV38-110_GTGAAA_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1652	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22195
WRN_BGKLV38-110_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1652					GRCh38	V40	WRN_BGKLV38-110_GTGAAA_L008_001.R1.fastq.gz,WRN_BGKLV38-110_GTGAAA_L008_001.R2.fastq.gz		ENCORE2	22207
WRN_BGKLV38-110_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1652					GRCh38	V40	WRN_BGKLV38-110/Aligned.sortedByCoord.out.bam		ENCORE2	22219
WRN_BGKLV38-110_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1652					GRCh38	V40	WRN_BGKLV38-110/Aligned.sortedByCoord.out.bam		ENCORE2	22231
WRN_BGKLV38-110_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1652					GRCh38	V40	WRN_BGKLV38-110/Aligned.sortedByCoord.out.bam		ENCORE2	22243
WRN_BGKLV38-110_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1652					GRCh38	V40	WRN_BGKLV38-110/Aligned.sortedByCoord.out.bam		ENCORE2	22255
WRN_BGKLV38-110_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1652					GRCh38	V40	WRN_BGKLV38-110_GTGAAA_L008_001.R1.fastq.gz,WRN_BGKLV38-110_GTGAAA_L008_001.R2.fastq.gz		ENCORE2	22267