MATR3 RNA-Seq in HepG2

General Information


RBP	MATR3
Cell_Line	HepG2
Method	shRNA
Exp_Name	MATR3-BGHLV12-HepG2
ENCODE_series_ID	ENCSR875WKW
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR492UFS
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	MATR3_17-BGHLV12-49
Rep2	MATR3_17-BGHLV12-50
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	57.0
Rep2_qPCR	64.9
Rep1_WB	no clear band
Rep2_WB	no clear band
Antibody Cat#	ab151714
Antibody Lot#	GR108745-9
Antibody DCC ID	ENCAB789SRM
Status	Released
Project	ENCODE3
ID	345

Experiment Information (Status: Released)

	BGHLV12-49	BGHLV12-50
idx	49	50
TRCN#_or_BGC#	TRCN0000293617	TRCN0000293617
shRNA_or_gRNA_sequence	TGACTTCCTAAGCTACTTAAG	TGACTTCCTAAGCTACTTAAG
PAM
Name	MATR3_17	MATR3_17
Sample_ID	BGHLV12-49	BGHLV12-50
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	MATR3	MATR3
qPCR_result	57.0	64.9
Ave_qPCR	61.0
RT-qPCR_primer-F	TGGTTCTGAGGATTCCAAACA
RT-qPCR_primer-R	TTGGAGATTCTTTGCCATCTG
protein_conc	1225	2350
WB_result	no clear band	no clear band
Ave_WB
WB_DONE_date	2/25/16	wes
MW	95kda
IP
antibody_Cat#	ab151714	ab151714
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	75	0
Rep2_TPM	74.5	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2096	2097

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV12-49	BGHLV12-50
Sample_ID	BGHLV12-49	BGHLV12-50
Sample Name	MATR3_17-BGHLV12-49	MATR3_17-BGHLV12-50
Sample Name	MATR3_17-BGHLV12-49	MATR3_17-BGHLV12-50
RBP	MATR3	MATR3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	404	405

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-49	BGHLV12-50
Sample #
Sample Name	MATR3-BGHLV12-49	MATR3-BGHLV12-50
Sample_Name_Alias	MATR3_17-BGHLV12-49	MATR3_17-BGHLV12-50
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/E1.png	DNA_Library_LV12/set3/F1.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_LV12/set1/E5.png	RNA_Library_LV12/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-49	BGHLV12-50
RBP	MATR3	MATR3
Batch_ID	BGHLV12	BGHLV12
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2028	2029

Sequencing Information

	BGHLV12-49	BGHLV12-50
Sample_ID	BGHLV12-49	BGHLV12-50
Sample Name	MATR3_17-BGHLV12-49	MATR3_17-BGHLV12-50
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	63,750,000	65,410,000
total_aligned_reads	57,960,218	59,749,168
unique_aligned_reads	54,915,242	56,579,538
percent_uniqueAligned	0.86142	0.86500
correlation_replicates	0.997542	0.997542
spikein_reads	327,062	347,208
percent_spikeins	0.00513	0.00531
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	728	729

Data Submission Information

	BGHLV12-49	BGHLV12-49
ENCODE_alias	brenton-graveley:MATR3-17-BGHLV12	brenton-graveley:MATR3-BGHLV12-HepG2
ENCODE_accession	ENCSR492UFS	ENCSR875WKW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-49	BGHLV12-49
Sample Name	MATR3_17-BGHLV12-49	MATR3_17-BGHLV12-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2751	6807

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
MATR3_17-BGHLV12-49_AGTCAA_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	728	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12785
MATR3_17-BGHLV12-49_AGTCAA_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	728	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12854
MATR3_17-BGHLV12-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	728					GRCh38	V40	MATR3_17-BGHLV12-49_AGTCAA_L006_R1_001.fastq.gz,MATR3_17-BGHLV12-49_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	12924
MATR3_17-BGHLV12-49_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	728					GRCh38	V40	MATR3_17-BGHLV12-49/Aligned.sortedByCoord.out.bam		ENCORE2	12994
MATR3_17-BGHLV12-49_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	728					GRCh38	V40	MATR3_17-BGHLV12-49/Aligned.sortedByCoord.out.bam		ENCORE2	13064
MATR3_17-BGHLV12-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	728					GRCh38	V40	MATR3_17-BGHLV12-49/Aligned.sortedByCoord.out.bam		ENCORE2	13134
MATR3_17-BGHLV12-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	728					GRCh38	V40	MATR3_17-BGHLV12-49/Aligned.sortedByCoord.out.bam		ENCORE2	13204
MATR3_17-BGHLV12-49_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	728					GRCh38	V40	MATR3_17-BGHLV12-49_AGTCAA_L006_R1_001.fastq.gz,MATR3_17-BGHLV12-49_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	13274
MATR3_17-BGHLV12-50_AGTTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	729	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12786
MATR3_17-BGHLV12-50_AGTTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	729	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12855
MATR3_17-BGHLV12-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	729					GRCh38	V40	MATR3_17-BGHLV12-50_AGTTCC_L006_R1_001.fastq.gz,MATR3_17-BGHLV12-50_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	12925
MATR3_17-BGHLV12-50_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	729					GRCh38	V40	MATR3_17-BGHLV12-50/Aligned.sortedByCoord.out.bam		ENCORE2	12995
MATR3_17-BGHLV12-50_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	729					GRCh38	V40	MATR3_17-BGHLV12-50/Aligned.sortedByCoord.out.bam		ENCORE2	13065
MATR3_17-BGHLV12-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	729					GRCh38	V40	MATR3_17-BGHLV12-50/Aligned.sortedByCoord.out.bam		ENCORE2	13135
MATR3_17-BGHLV12-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	729					GRCh38	V40	MATR3_17-BGHLV12-50/Aligned.sortedByCoord.out.bam		ENCORE2	13205
MATR3_17-BGHLV12-50_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	729					GRCh38	V40	MATR3_17-BGHLV12-50_AGTTCC_L006_R1_001.fastq.gz,MATR3_17-BGHLV12-50_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	13275