AUH RNA-Seq in K562

General Information


RBP	AUH
Cell_Line	K562
Method	shRNA
Exp_Name	AUH-BGKLV38-K562
ENCODE_series_ID	ENCSR805AKV
Batch_ID	BGKLV38
Pool ID	Pool-161129
Local_Set_Name	set38
ENCODE_KD_Exp_ID	ENCSR395FYF
ENCODE_CN_Exp_ID	ENCSR718EWL
Rep1	AUH_BGKLV38-27
Rep2	AUH_BGKLV38-28
CN1	NT_BGKLV38-1
CN2	NT_BGKLV38-2
Rep1_qPCR	45.7
Rep2_qPCR	56.1
Rep1_WB	84.4
Rep2_WB	63.4
Antibody Cat#	RN037P
Antibody Lot#	RN037P
Antibody DCC ID	ENCAB000BFE
Status	Released
Project	ENCODE3
ID	756

Experiment Information (Status: Released)

	BGKLV38-27	BGKLV38-28
idx	798	799
TRCN#_or_BGC#	TRCN0000052449	TRCN0000052449
shRNA_or_gRNA_sequence	CCGTCCTATCACCGTATCTTA	CCGTCCTATCACCGTATCTTA
PAM
Name	AUH	AUH
Sample_ID	BGKLV38-27	BGKLV38-28
transduction_Date	9/15/16	9/15/16
days
RBP_name	AUH	AUH
qPCR_result	45.7	56.1
Ave_qPCR	50.9
RT-qPCR_primer-F	aggtggtggtcttgaactgg
RT-qPCR_primer-R	caccaggaataatcgccaat
protein_conc	2927	2537
WB_result	84.4	63.4
Ave_WB	73.9
WB_DONE_date	9/30/16	wes
MW	36kDa
IP	1IP	1IP
antibody_Cat#	RN037P	RN037P
Antibody DCC ID	ENCAB000BFE	ENCAB000BFE
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	891	892

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AUH	Product_ID: RN037P Lot_ID: 1 Source: MBLI Target Name: AUH-human

Experiment Status

	BGKLV38-27	BGKLV38-28
Sample_ID	BGKLV38-27	BGKLV38-28
Sample Name	AUH_BGKLV38-27	AUH_BGKLV38-28
Sample Name	AUH_BGKLV38-27	AUH_BGKLV38-28
RBP	AUH	AUH
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1307	1308

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-27	BGKLV38-28
Sample #
Sample Name	AUH-BGKLV38-27	AUH-BGKLV38-28
Sample_Name_Alias	AUH_BGKLV38-27	AUH_BGKLV38-28
Index Well Position	S13	S14
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/E5.png	DNA_Library_LV37-38/set1/F5.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV37_38/set1/E3.png	RNA_Library_LV37_38/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV38-27	BGKLV38-28
RBP	AUH	AUH
Batch_ID	BGKLV38	BGKLV38
WB_result	84.400	63.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2996	2997

Sequencing Information

	BGKLV38-27	BGKLV38-28
Sample_ID	BGKLV38-27	BGKLV38-28
Sample Name	AUH_BGKLV38-27	AUH_BGKLV38-28
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set38	set38
total_reads	98,027,734	90,091,728
total_aligned_reads	93,407,198	86,007,840
unique_aligned_reads	85,955,356	79,076,670
percent_uniqueAligned	0.87685	0.87774
correlation_replicates	0.997390	0.997390
spikein_reads	161,560	190,666
percent_spikeins	0.00165	0.00212
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1645	1646

Data Submission Information

	BGKLV38-27	BGKLV38-27
ENCODE_alias	brenton-graveley:AUH_BGKLV38	brenton-graveley:AUH-BGKLV38-K562
ENCODE_accession	ENCSR395FYF	ENCSR805AKV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV38-27	BGKLV38-27
Sample Name	AUH_BGKLV38-27	AUH_BGKLV38-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3193	6599

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
AUH_BGKLV38-27_AGTCAA_L007_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1645	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22176
AUH_BGKLV38-27_AGTCAA_L007_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1645	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22188
AUH_BGKLV38-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1645					GRCh38	V40	AUH_BGKLV38-27_AGTCAA_L007_001.R1.fastq.gz,AUH_BGKLV38-27_AGTCAA_L007_001.R2.fastq.gz		ENCORE2	22200
AUH_BGKLV38-27_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	1645					GRCh38	V40	AUH_BGKLV38-27/Aligned.sortedByCoord.out.bam		ENCORE2	22212
AUH_BGKLV38-27_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	1645					GRCh38	V40	AUH_BGKLV38-27/Aligned.sortedByCoord.out.bam		ENCORE2	22224
AUH_BGKLV38-27_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	1645					GRCh38	V40	AUH_BGKLV38-27/Aligned.sortedByCoord.out.bam		ENCORE2	22236
AUH_BGKLV38-27_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	1645					GRCh38	V40	AUH_BGKLV38-27/Aligned.sortedByCoord.out.bam		ENCORE2	22248
AUH_BGKLV38-27_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1645					GRCh38	V40	AUH_BGKLV38-27_AGTCAA_L007_001.R1.fastq.gz,AUH_BGKLV38-27_AGTCAA_L007_001.R2.fastq.gz		ENCORE2	22260
AUH_BGKLV38-28_AGTTCC_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1646	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22177
AUH_BGKLV38-28_AGTTCC_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1646	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22189
AUH_BGKLV38-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1646					GRCh38	V40	AUH_BGKLV38-28_AGTTCC_L008_001.R1.fastq.gz,AUH_BGKLV38-28_AGTTCC_L008_001.R2.fastq.gz		ENCORE2	22201
AUH_BGKLV38-28_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	1646					GRCh38	V40	AUH_BGKLV38-28/Aligned.sortedByCoord.out.bam		ENCORE2	22213
AUH_BGKLV38-28_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	1646					GRCh38	V40	AUH_BGKLV38-28/Aligned.sortedByCoord.out.bam		ENCORE2	22225
AUH_BGKLV38-28_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	1646					GRCh38	V40	AUH_BGKLV38-28/Aligned.sortedByCoord.out.bam		ENCORE2	22237
AUH_BGKLV38-28_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	1646					GRCh38	V40	AUH_BGKLV38-28/Aligned.sortedByCoord.out.bam		ENCORE2	22249
AUH_BGKLV38-28_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1646					GRCh38	V40	AUH_BGKLV38-28_AGTTCC_L008_001.R1.fastq.gz,AUH_BGKLV38-28_AGTTCC_L008_001.R2.fastq.gz		ENCORE2	22261