MSI2 RNA-Seq in HepG2

General Information


RBP	MSI2
Cell_Line	HepG2
Method	shRNA
Exp_Name	MSI2-BGHLV30-HepG2
ENCODE_series_ID	ENCSR198YXM
Batch_ID	BGHLV30
Pool ID	Pool-151215A
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR896MMU
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	MSI2_BGHLV30-43
Rep2	MSI2_BGHLV30-44
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	74.8
Rep2_qPCR	78.0
Rep1_WB	68.1
Rep2_WB	73.6
Antibody Cat#	GTX117808
Antibody Lot#	GTX117808
Antibody DCC ID	ENCAB529VOS
Status	Released
Project	ENCODE3
ID	681

Experiment Information (Status: Released)

	BGHLV30-43	BGHLV30-44
idx	731	732
TRCN#_or_BGC#	TRCN0000062809	TRCN0000062809
shRNA_or_gRNA_sequence	GTGGAAGATGTAAAGCAATAT	GTGGAAGATGTAAAGCAATAT
PAM
Name	MSI2	MSI2
Sample_ID	BGHLV30-43	BGHLV30-44
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	MSI2	MSI2
qPCR_result	74.8	78.0
Ave_qPCR	76.4
RT-qPCR_primer-F	ATTGAGCAGGTGCTTTCGTT
RT-qPCR_primer-R	CTCAGAAACTTCGCCCAGTC
protein_conc	4309	5097
WB_result	68.1	73.6
Ave_WB	70.9
WB_DONE_date	9/16/2015
MW	35kDa
IP	1MB	1MB
antibody_Cat#	GTX117808	GTX117808
Antibody DCC ID	ENCAB529VOS	ENCAB529VOS
submitted_to_DCC_date	12/7/2015
Rep1_TPM	26.7	0
Rep2_TPM	29.8	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2818	2819

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

	BGHLV30-43	BGHLV30-44
Sample_ID	BGHLV30-43	BGHLV30-44
Sample Name	MSI2_BGHLV30-43	MSI2_BGHLV30-44
Sample Name	MSI2_BGHLV30-43	MSI2_BGHLV30-44
RBP	MSI2	MSI2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1060	1061

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-43	BGHLV30-44
Sample #
Sample Name	MSI2-BGHLV30-43	MSI2-BGHLV30-44
Sample_Name_Alias	MSI2_BGHLV30-43	MSI2_BGHLV30-44
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E11.png	DNA_Library_LV28-29-30/set1/F11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G6.png	RNA_Library_LV29-30-31-32/set1/H6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-43	BGHLV30-44
RBP	MSI2	MSI2
Batch_ID	BGHLV30	BGHLV30
WB_result	68.100	73.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2752	2753

Sequencing Information

	BGHLV30-43	BGHLV30-44
Sample_ID	BGHLV30-43	BGHLV30-44
Sample Name	MSI2_BGHLV30-43	MSI2_BGHLV30-44
Pool ID	Pool-151215A	Pool-151215A
LocalServer_folder	set30	set30
total_reads	86,461,380	70,495,262
total_aligned_reads	69,915,596	56,759,908
unique_aligned_reads	65,742,822	53,417,742
percent_uniqueAligned	0.76037	0.75775
correlation_replicates	0.999376	0.999376
spikein_reads	260,068	185,434
percent_spikeins	0.00301	0.00263
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1372	1373

Data Submission Information

	BGHLV30-43	BGHLV30-43
ENCODE_alias	brenton-graveley:MSI2_BGHLV30	brenton-graveley:MSI2-BGHLV30-HepG2
ENCODE_accession	ENCSR896MMU	ENCSR198YXM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-43	BGHLV30-43
Sample Name	MSI2_BGHLV30-43	MSI2_BGHLV30-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3079	6812

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_BGHLV30-43_AGTCAA_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1372	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20718
MSI2_BGHLV30-43_AGTCAA_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1372	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20752
MSI2_BGHLV30-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1372					GRCh38	V40	MSI2_BGHLV30-43_AGTCAA_L002_001.R1.fastq.gz,MSI2_BGHLV30-43_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	20786
MSI2_BGHLV30-43_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1372					GRCh38	V40	MSI2_BGHLV30-43/Aligned.sortedByCoord.out.bam		ENCORE2	20820
MSI2_BGHLV30-43_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1372					GRCh38	V40	MSI2_BGHLV30-43/Aligned.sortedByCoord.out.bam		ENCORE2	20854
MSI2_BGHLV30-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1372					GRCh38	V40	MSI2_BGHLV30-43/Aligned.sortedByCoord.out.bam		ENCORE2	20888
MSI2_BGHLV30-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1372					GRCh38	V40	MSI2_BGHLV30-43/Aligned.sortedByCoord.out.bam		ENCORE2	20922
MSI2_BGHLV30-43_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1372					GRCh38	V40	MSI2_BGHLV30-43_AGTCAA_L002_001.R1.fastq.gz,MSI2_BGHLV30-43_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	20956
MSI2_BGHLV30-44_AGTTCC_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1373	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20719
MSI2_BGHLV30-44_AGTTCC_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1373	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20753
MSI2_BGHLV30-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1373					GRCh38	V40	MSI2_BGHLV30-44_AGTTCC_L002_001.R1.fastq.gz,MSI2_BGHLV30-44_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	20787
MSI2_BGHLV30-44_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1373					GRCh38	V40	MSI2_BGHLV30-44/Aligned.sortedByCoord.out.bam		ENCORE2	20821
MSI2_BGHLV30-44_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1373					GRCh38	V40	MSI2_BGHLV30-44/Aligned.sortedByCoord.out.bam		ENCORE2	20855
MSI2_BGHLV30-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1373					GRCh38	V40	MSI2_BGHLV30-44/Aligned.sortedByCoord.out.bam		ENCORE2	20889
MSI2_BGHLV30-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1373					GRCh38	V40	MSI2_BGHLV30-44/Aligned.sortedByCoord.out.bam		ENCORE2	20923
MSI2_BGHLV30-44_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1373					GRCh38	V40	MSI2_BGHLV30-44_AGTTCC_L002_001.R1.fastq.gz,MSI2_BGHLV30-44_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	20957