DROSHA RNA-Seq in K562

General Information


RBP	DROSHA
Cell_Line	K562
Method	shRNA
Exp_Name	DROSHA-BGKLV28-K562
ENCODE_series_ID	ENCSR317AOL
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR624XHG
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	RNASEN50_BGKLV28-45
Rep2	RNASEN50_BGKLV28-46
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	60.9
Rep2_qPCR	54.5
Rep1_WB	68.6
Rep2_WB	71.4
Antibody Cat#	A301-886A
Antibody Lot#	A301-886A
Antibody DCC ID	ENCAB936LAQ
Status	Released
Project	ENCODE3
ID	655

Experiment Information (Status: Released)

	BGKLV28-45	BGKLV28-46
idx	514	515
TRCN#_or_BGC#	TRCN0000022250	TRCN0000022250
shRNA_or_gRNA_sequence	CGAAGCTCTTTGGTGAATAAT	CGAAGCTCTTTGGTGAATAAT
PAM
Name	RNASEN_50	RNASEN_50
Sample_ID	BGKLV28-45	BGKLV28-46
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	DROSHA	DROSHA
qPCR_result	60.9	54.5
Ave_qPCR	57.7
RT-qPCR_primer-F	aggccagatgaatgatggac
RT-qPCR_primer-R	cttgatggcctcttctccag
protein_conc	2851	2594
WB_result	68.6	71.4
Ave_WB	70.0	very light band
WB_DONE_date	8/19/2015
MW	159kDa
IP	1IP	1IP
antibody_Cat#	A301-886A	A301-886A
Antibody DCC ID	ENCAB936LAQ
submitted_to_DCC_date	12/7/2015
Rep1_TPM	43.4109539	0
Rep2_TPM	29.8305427	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	589	590

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DROSHA	Product_ID: A301-886A Lot_ID: 1 Source: Bethyl Labs Target Name: DROSHA-human

Experiment Status

	BGKLV28-45	BGKLV28-46
Sample_ID	BGKLV28-45	BGKLV28-46
Sample Name	RNASEN50_BGKLV28-45	RNASEN50_BGKLV28-46
Sample Name	RNASEN50_BGKLV28-45	RNASEN50_BGKLV28-46
RBP	DROSHA	DROSHA
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	996	997

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-45	BGKLV28-46
Sample #
Sample Name	DROSHA-BGKLV28-45	DROSHA-BGKLV28-46
Sample_Name_Alias	RNASEN50_BGKLV28-45	RNASEN50_BGKLV28-46
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A3.png	DNA_Library_LV28-29-30/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E8.png	RNA_Library_LV26-27-28-29/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-45	BGKLV28-46
RBP	DROSHA	DROSHA
Batch_ID	BGKLV28	BGKLV28
WB_result	68.600	71.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2688	2689

Sequencing Information

	BGKLV28-45	BGKLV28-46
Sample_ID	BGKLV28-45	BGKLV28-46
Sample Name	RNASEN50_BGKLV28-45	RNASEN50_BGKLV28-46
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	86,468,396	100,101,938
total_aligned_reads	77,171,690	91,071,392
unique_aligned_reads	69,901,386	82,934,154
percent_uniqueAligned	0.80840	0.82850
correlation_replicates	0.991588	0.991588
spikein_reads	277,692	329,394
percent_spikeins	0.00321	0.00329
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1330	1331

Data Submission Information

	BGKLV28-45	BGKLV28-45
ENCODE_alias	brenton-graveley:RNASEN50_BGKLV28	brenton-graveley:DROSHA-BGKLV28-K562
ENCODE_accession	ENCSR624XHG	ENCSR317AOL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-45	BGKLV28-45
Sample Name	RNASEN50_BGKLV28-45	RNASEN50_BGKLV28-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3047	6673

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
RNASEN50_BGKLV28-45_GTCCGC_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1330	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20174
RNASEN50_BGKLV28-45_GTCCGC_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1330	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20206
RNASEN50_BGKLV28-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1330					GRCh38	V40	RNASEN50_BGKLV28-45_GTCCGC_L001_001.R1.fastq.gz,RNASEN50_BGKLV28-45_GTCCGC_L001_001.R2.fastq.gz		ENCORE2	20238
RNASEN50_BGKLV28-45_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1330					GRCh38	V40	RNASEN50_BGKLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	20270
RNASEN50_BGKLV28-45_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1330					GRCh38	V40	RNASEN50_BGKLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	20302
RNASEN50_BGKLV28-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1330					GRCh38	V40	RNASEN50_BGKLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	20334
RNASEN50_BGKLV28-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1330					GRCh38	V40	RNASEN50_BGKLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	20366
RNASEN50_BGKLV28-45_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1330					GRCh38	V40	RNASEN50_BGKLV28-45_GTCCGC_L001_001.R1.fastq.gz,RNASEN50_BGKLV28-45_GTCCGC_L001_001.R2.fastq.gz		ENCORE2	20398
RNASEN50_BGKLV28-46_GTGAAA_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1331	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20175
RNASEN50_BGKLV28-46_GTGAAA_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1331	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20207
RNASEN50_BGKLV28-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1331					GRCh38	V40	RNASEN50_BGKLV28-46_GTGAAA_L001_001.R1.fastq.gz,RNASEN50_BGKLV28-46_GTGAAA_L001_001.R2.fastq.gz		ENCORE2	20239
RNASEN50_BGKLV28-46_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1331					GRCh38	V40	RNASEN50_BGKLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	20271
RNASEN50_BGKLV28-46_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1331					GRCh38	V40	RNASEN50_BGKLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	20303
RNASEN50_BGKLV28-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1331					GRCh38	V40	RNASEN50_BGKLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	20335
RNASEN50_BGKLV28-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1331					GRCh38	V40	RNASEN50_BGKLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	20367
RNASEN50_BGKLV28-46_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1331					GRCh38	V40	RNASEN50_BGKLV28-46_GTGAAA_L001_001.R1.fastq.gz,RNASEN50_BGKLV28-46_GTGAAA_L001_001.R2.fastq.gz		ENCORE2	20399