MSI2 RNA-Seq in K562

General Information


RBP	MSI2
Cell_Line	K562
Method	shRNA
Exp_Name	MSI2-BGKLV25-K562
ENCODE_series_ID	ENCSR849GEE
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR169QQW
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	MSI2_BGKLV25-33
Rep2	MSI2_BGKLV25-34
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	70.4
Rep2_qPCR	70.9
Rep1_WB	82.0
Rep2_WB	90.9
Antibody Cat#	GTX117808
Antibody Lot#	GTX117808
Antibody DCC ID	ENCAB529VOS
Status	Released
Project	ENCODE3
ID	619

Experiment Information (Status: Released)

	BGKLV25-33	BGKLV25-34
idx	436	437
TRCN#_or_BGC#	TRCN0000062812	TRCN0000062812
shRNA_or_gRNA_sequence	AGATAGCCTTAGAGACTATTT	AGATAGCCTTAGAGACTATTT
PAM
Name	MSI2	MSI2
Sample_ID	BGKLV25-33	BGKLV25-34
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	MSI2	MSI2
qPCR_result	70.4	70.9
Ave_qPCR	70.7
RT-qPCR_primer-F	ATTGAGCAGGTGCTTTCGTT
RT-qPCR_primer-R	CTCAGAAACTTCGCCCAGTC
protein_conc	4269	5676
WB_result	82.0	90.9
Ave_WB	86.5
WB_DONE_date	3/30/2015
MW	35kDa
IP	1MB	1MB
antibody_Cat#	GTX117808	GTX117808
Antibody DCC ID	ENCAB529VOS	ENCAB529VOS
submitted_to_DCC_date	5/4/2015
Rep1_TPM	8.28794522	0
Rep2_TPM	6.2251393	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	507	508

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MSI2	Product_ID: GTX117808 Lot_ID: 40415 Source: GeneTex Target Name: MSI2-human

Experiment Status

	BGKLV25-33	BGKLV25-34
Sample_ID	BGKLV25-33	BGKLV25-34
Sample Name	MSI2_BGKLV25-33	MSI2_BGKLV25-34
Sample Name	MSI2_BGKLV25-33	MSI2_BGKLV25-34
RBP	MSI2	MSI2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	916	917

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-33	BGKLV25-34
Sample #
Sample Name	MSI2-BGKLV25-33	MSI2-BGKLV25-34
Sample_Name_Alias	MSI2_BGKLV25-33	MSI2_BGKLV25-34
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G2.png	DNA_Library_LV24-25-26/set1/H2.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A11.png	RNA_Library_LV22-23-25/set1/B11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-33	BGKLV25-34
RBP	MSI2	MSI2
Batch_ID	BGKLV25	BGKLV25
WB_result	82.000	90.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2608	2609

Sequencing Information

	BGKLV25-33	BGKLV25-34
Sample_ID	BGKLV25-33	BGKLV25-34
Sample Name	MSI2_BGKLV25-33	MSI2_BGKLV25-34
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	82,622,782	106,355,376
total_aligned_reads	84,212,402	108,969,770
unique_aligned_reads	76,896,046	99,133,578
percent_uniqueAligned	0.93069	0.93210
correlation_replicates	0.997201	0.997201
spikein_reads	513,346	725,056
percent_spikeins	0.00621	0.00682
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1250	1251

Data Submission Information

	BGKLV25-33	BGKLV25-33
ENCODE_alias	brenton-graveley:MSI2_BGKLV25	brenton-graveley:MSI2-BGKLV25-K562
ENCODE_accession	ENCSR169QQW	ENCSR849GEE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-33	BGKLV25-33
Sample Name	MSI2_BGKLV25-33	MSI2_BGKLV25-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3007	6813

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
MSI2_BGKLV25-33_ACTGAT_L006_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1250	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19576
MSI2_BGKLV25-33_ACTGAT_L006_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1250	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19612
MSI2_BGKLV25-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1250					GRCh38	V40	MSI2_BGKLV25-33_ACTGAT_L006_001.R1.fastq.gz,MSI2_BGKLV25-33_ACTGAT_L006_001.R2.fastq.gz		ENCORE2	19648
MSI2_BGKLV25-33_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1250					GRCh38	V40	MSI2_BGKLV25-33/Aligned.sortedByCoord.out.bam		ENCORE2	19684
MSI2_BGKLV25-33_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1250					GRCh38	V40	MSI2_BGKLV25-33/Aligned.sortedByCoord.out.bam		ENCORE2	19720
MSI2_BGKLV25-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1250					GRCh38	V40	MSI2_BGKLV25-33/Aligned.sortedByCoord.out.bam		ENCORE2	19756
MSI2_BGKLV25-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1250					GRCh38	V40	MSI2_BGKLV25-33/Aligned.sortedByCoord.out.bam		ENCORE2	19792
MSI2_BGKLV25-33_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1250					GRCh38	V40	MSI2_BGKLV25-33_ACTGAT_L006_001.R1.fastq.gz,MSI2_BGKLV25-33_ACTGAT_L006_001.R2.fastq.gz		ENCORE2	19982
MSI2_BGKLV25-34_ATTCCT_L006_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1251	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19577
MSI2_BGKLV25-34_ATTCCT_L006_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1251	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19613
MSI2_BGKLV25-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1251					GRCh38	V40	MSI2_BGKLV25-34_ATTCCT_L006_001.R1.fastq.gz,MSI2_BGKLV25-34_ATTCCT_L006_001.R2.fastq.gz		ENCORE2	19649
MSI2_BGKLV25-34_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1251					GRCh38	V40	MSI2_BGKLV25-34/Aligned.sortedByCoord.out.bam		ENCORE2	19685
MSI2_BGKLV25-34_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1251					GRCh38	V40	MSI2_BGKLV25-34/Aligned.sortedByCoord.out.bam		ENCORE2	19721
MSI2_BGKLV25-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1251					GRCh38	V40	MSI2_BGKLV25-34/Aligned.sortedByCoord.out.bam		ENCORE2	19757
MSI2_BGKLV25-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1251					GRCh38	V40	MSI2_BGKLV25-34/Aligned.sortedByCoord.out.bam		ENCORE2	19793
MSI2_BGKLV25-34_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1251					GRCh38	V40	MSI2_BGKLV25-34_ATTCCT_L006_001.R1.fastq.gz,MSI2_BGKLV25-34_ATTCCT_L006_001.R2.fastq.gz		ENCORE2	19983