MTPAP RNA-Seq in HepG2

General Information


RBP	MTPAP
Cell_Line	HepG2
Method	shRNA
Exp_Name	MTPAP-BGHLV35-HepG2
ENCODE_series_ID	ENCSR326YSW
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR701GSV
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	MTPAP_BGHLV35-27
Rep2	MTPAP_BGHLV35-28
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	64.4
Rep2_qPCR	70.3
Rep1_WB	52.9
Rep2_WB	51.5
Antibody Cat#	A303-904A
Antibody Lot#	A303-904A
Antibody DCC ID	ENCAB235DTM
Status	Released
Project	ENCODE3
ID	736

Experiment Information (Status: Released)

	BGHLV35-27	BGHLV35-28
idx	883	884
TRCN#_or_BGC#	TRCN0000160601	TRCN0000160601
shRNA_or_gRNA_sequence	CGACCTTCCATATCAAGTAAT	CGACCTTCCATATCAAGTAAT
PAM
Name	MTPAP	MTPAP
Sample_ID	BGHLV35-27	BGHLV35-28
transduction_Date	4/29/16	4/29/16
days
RBP_name	MTPAP	MTPAP
qPCR_result	64.4	70.3
Ave_qPCR	67.4
RT-qPCR_primer-F	ttggcaattttgctttcgat
RT-qPCR_primer-R	tggattctgaatgtacagaggaga
protein_conc	3655	3758
WB_result	52.9	51.5
Ave_WB	52.2
WB_DONE_date	5/23/16
MW	66kDa
IP	1	1
antibody_Cat#	A303-904A	A303-904A
Antibody DCC ID	ENCAB235DTM	ENCAB235DTM
submitted_to_DCC_date	10/26/16
Rep1_TPM	4.8	4.8
Rep2_TPM	4.2	4.2
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2972	2973

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MTPAP	Product_ID: A303-904A Lot_ID: 1 Source: Bethyl Labs Target Name: MTPAP-human

Experiment Status

	BGHLV35-27	BGHLV35-28
Sample_ID	BGHLV35-27	BGHLV35-28
Sample Name	MTPAP_BGHLV35-27	MTPAP_BGHLV35-28
Sample Name	MTPAP_BGHLV35-27	MTPAP_BGHLV35-28
RBP	MTPAP	MTPAP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1261	1262

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-27	BGHLV35-28
Sample #
Sample Name	MTPAP-BGHLV35-27	MTPAP-BGHLV35-28
Sample_Name_Alias	MTPAP_BGHLV35-27	MTPAP_BGHLV35-28
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/G2.png	DNA_Library_LV35/set2/H2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/G2.png	RNA_Library_LV35_LV36/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-27	BGHLV35-28
RBP	MTPAP	MTPAP
Batch_ID	BGHLV35	BGHLV35
WB_result	52.900	51.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2946	2947

Sequencing Information

	BGHLV35-27	BGHLV35-28
Sample_ID	BGHLV35-27	BGHLV35-28
Sample Name	MTPAP_BGHLV35-27	MTPAP_BGHLV35-28
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	81,211,066	72,567,608
total_aligned_reads	61,563,778	52,035,980
unique_aligned_reads	58,071,044	49,229,126
percent_uniqueAligned	0.71506	0.67839
correlation_replicates	0.973490	0.973490
spikein_reads	124,472	124,474
percent_spikeins	0.00153	0.00172
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1595	1596

Data Submission Information

	BGHLV35-27	BGHLV35-27
ENCODE_alias	brenton-graveley:MTPAP_BGHLV35	brenton-graveley:MTPAP-BGHLV35-HepG2
ENCODE_accession	ENCSR701GSV	ENCSR326YSW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-27	BGHLV35-27
Sample Name	MTPAP_BGHLV35-27	MTPAP_BGHLV35-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3170	6814

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
MTPAP_BGHLV35-27_ATGTCA_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1595	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21694
MTPAP_BGHLV35-27_ATGTCA_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1595	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21720
MTPAP_BGHLV35-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1595					GRCh38	V40	MTPAP_BGHLV35-27_ATGTCA_L006_001.R1.fastq.gz,MTPAP_BGHLV35-27_ATGTCA_L006_001.R2.fastq.gz		ENCORE2	21746
MTPAP_BGHLV35-27_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1595					GRCh38	V40	MTPAP_BGHLV35-27/Aligned.sortedByCoord.out.bam		ENCORE2	21772
MTPAP_BGHLV35-27_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1595					GRCh38	V40	MTPAP_BGHLV35-27/Aligned.sortedByCoord.out.bam		ENCORE2	21798
MTPAP_BGHLV35-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1595					GRCh38	V40	MTPAP_BGHLV35-27/Aligned.sortedByCoord.out.bam		ENCORE2	21824
MTPAP_BGHLV35-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1595					GRCh38	V40	MTPAP_BGHLV35-27/Aligned.sortedByCoord.out.bam		ENCORE2	21850
MTPAP_BGHLV35-27_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1595					GRCh38	V40	MTPAP_BGHLV35-27_ATGTCA_L006_001.R1.fastq.gz,MTPAP_BGHLV35-27_ATGTCA_L006_001.R2.fastq.gz		ENCORE2	21876
MTPAP_BGHLV35-28_CCGTCC_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1596	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21695
MTPAP_BGHLV35-28_CCGTCC_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1596	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21721
MTPAP_BGHLV35-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1596					GRCh38	V40	MTPAP_BGHLV35-28_CCGTCC_L006_001.R1.fastq.gz,MTPAP_BGHLV35-28_CCGTCC_L006_001.R2.fastq.gz		ENCORE2	21747
MTPAP_BGHLV35-28_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1596					GRCh38	V40	MTPAP_BGHLV35-28/Aligned.sortedByCoord.out.bam		ENCORE2	21773
MTPAP_BGHLV35-28_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1596					GRCh38	V40	MTPAP_BGHLV35-28/Aligned.sortedByCoord.out.bam		ENCORE2	21799
MTPAP_BGHLV35-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1596					GRCh38	V40	MTPAP_BGHLV35-28/Aligned.sortedByCoord.out.bam		ENCORE2	21825
MTPAP_BGHLV35-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1596					GRCh38	V40	MTPAP_BGHLV35-28/Aligned.sortedByCoord.out.bam		ENCORE2	21851
MTPAP_BGHLV35-28_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1596					GRCh38	V40	MTPAP_BGHLV35-28_CCGTCC_L006_001.R1.fastq.gz,MTPAP_BGHLV35-28_CCGTCC_L006_001.R2.fastq.gz		ENCORE2	21877