MAGOH RNA-Seq in K562

General Information


RBP	MAGOH
Cell_Line	K562
Method	shRNA
Exp_Name	MAGOH-BGKLV11-K562
ENCODE_series_ID	ENCSR726JGY
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR849STR
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	MAGOH-LV11-25
Rep2	MAGOH-LV11-26
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	92.9
Rep2_qPCR	90.5
Rep1_WB	65.7
Rep2_WB	57.2
Antibody Cat#	RN089PW
Antibody Lot#	RN089PW
Antibody DCC ID	ENCAB122RRN
Status	Released
Project	ENCODE3
ID	314

Experiment Information (Status: Released)

	BGKLV11-25	BGKLV11-26
idx	94	95
TRCN#_or_BGC#	TRCN0000006614	TRCN0000006614
shRNA_or_gRNA_sequence	CCAGAAGGCTTACGAGTATTT	CCAGAAGGCTTACGAGTATTT
PAM
Name	MAGOH	MAGOH
Sample_ID	BGKLV11-25	BGKLV11-26
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	MAGOH	MAGOH
qPCR_result	92.9	90.5
Ave_qPCR	91.7
RT-qPCR_primer-F	CAAAAATTGGTTCCCTTATTGA
RT-qPCR_primer-R	AACACTTCAGGTCCTGGACAA
protein_conc	1567	1879
WB_result	65.7	57.2
Ave_WB	61.5
WB_DONE_date	6/19/2014
MW	17kDa
IP	1	1
antibody_Cat#	RN089PW	RN089PW
Antibody DCC ID	ENCAB122RRN	ENCAB122RRN
submitted_to_DCC_date	4/2/2015
Rep1_TPM	106.276282	0
Rep2_TPM	74.783799	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	107	108

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MAGOH	Product_ID: RN089PW Lot_ID: 1 Source: MBLI Target Name: MAGOH-human

Experiment Status

	BGKLV11-25	BGKLV11-26
Sample_ID	BGKLV11-25	BGKLV11-26
Sample Name	MAGOH-LV11-25	MAGOH-LV11-26
Sample Name	MAGOH-LV11-25	MAGOH-LV11-26
RBP	MAGOH	MAGOH
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	340	341

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-25	BGKLV11-26
Sample #
Sample Name	MAGOH-BGKLV11-25	MAGOH-BGKLV11-26
Sample_Name_Alias	MAGOH-LV11-25	MAGOH-LV11-26
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set2/E1.png	DNA_Library_LV11/set2/F1.png
RIN	9.0	9.0
libSample_RNA_Well	RNA_Library_LV11/set1/C3.png	RNA_Library_LV11/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-25	BGKLV11-26
RBP	MAGOH	MAGOH
Batch_ID	BGKLV11	BGKLV11
WB_result	65.700	57.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1962	1963

Sequencing Information

	BGKLV11-25	BGKLV11-26
Sample_ID	BGKLV11-25	BGKLV11-26
Sample Name	MAGOH-LV11-25	MAGOH-LV11-26
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	68,050,000	55,970,000
total_aligned_reads	54,754,812	45,570,870
unique_aligned_reads	50,252,592	41,828,590
percent_uniqueAligned	0.73847	0.74734
correlation_replicates	0.992604	0.992604
spikein_reads	526,032	355,938
percent_spikeins	0.00773	0.00636
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	662	663

Data Submission Information

	BGKLV11-25	BGKLV11-25
ENCODE_alias	brenton-graveley:MAGOH-LV11	brenton-graveley:MAGOH-BGKLV11-K562
ENCODE_accession	ENCSR849STR	ENCSR726JGY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-25	BGKLV11-25
Sample Name	MAGOH-LV11-25	MAGOH-LV11-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2719	6804

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
MAGOH-LV11-25_GTGGCC_L004_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	662	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12383
MAGOH-LV11-25_GTGGCC_L004_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	662	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12431
MAGOH-LV11-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	662					GRCh38	V40	MAGOH-LV11-25_GTGGCC_L004_R1_001.fastq.gz,MAGOH-LV11-25_GTGGCC_L004_R2_001.fastq.gz		ENCORE2	12479
MAGOH-LV11-25_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	662					GRCh38	V40	MAGOH-LV11-25/Aligned.sortedByCoord.out.bam		ENCORE2	12527
MAGOH-LV11-25_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	662					GRCh38	V40	MAGOH-LV11-25/Aligned.sortedByCoord.out.bam		ENCORE2	12575
MAGOH-LV11-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	662					GRCh38	V40	MAGOH-LV11-25/Aligned.sortedByCoord.out.bam		ENCORE2	12623
MAGOH-LV11-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	662					GRCh38	V40	MAGOH-LV11-25/Aligned.sortedByCoord.out.bam		ENCORE2	12671
MAGOH-LV11-25_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	662					GRCh38	V40	MAGOH-LV11-25_GTGGCC_L004_R1_001.fastq.gz,MAGOH-LV11-25_GTGGCC_L004_R2_001.fastq.gz		ENCORE2	12719
MAGOH-LV11-26_GTTTCG_L004_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	663	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12384
MAGOH-LV11-26_GTTTCG_L004_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	663	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12432
MAGOH-LV11-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	663					GRCh38	V40	MAGOH-LV11-26_GTTTCG_L004_R1_001.fastq.gz,MAGOH-LV11-26_GTTTCG_L004_R2_001.fastq.gz		ENCORE2	12480
MAGOH-LV11-26_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	663					GRCh38	V40	MAGOH-LV11-26/Aligned.sortedByCoord.out.bam		ENCORE2	12528
MAGOH-LV11-26_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	663					GRCh38	V40	MAGOH-LV11-26/Aligned.sortedByCoord.out.bam		ENCORE2	12576
MAGOH-LV11-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	663					GRCh38	V40	MAGOH-LV11-26/Aligned.sortedByCoord.out.bam		ENCORE2	12624
MAGOH-LV11-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	663					GRCh38	V40	MAGOH-LV11-26/Aligned.sortedByCoord.out.bam		ENCORE2	12672
MAGOH-LV11-26_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	663					GRCh38	V40	MAGOH-LV11-26_GTTTCG_L004_R1_001.fastq.gz,MAGOH-LV11-26_GTTTCG_L004_R2_001.fastq.gz		ENCORE2	12720