PPIG RNA-Seq in HepG2

General Information


RBP	PPIG
Cell_Line	HepG2
Method	shRNA
Exp_Name	PPIG-BGHLV27-HepG2
ENCODE_series_ID	ENCSR692CHB
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR620HAA
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	PPIG_BGHLV27-43
Rep2	PPIG_BGHLV27-44
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	64.1
Rep2_qPCR	55.8
Rep1_WB	83.1
Rep2_WB	87.4
Antibody Cat#	A302-075A
Antibody Lot#	A302-075A
Antibody DCC ID	ENCAB460YIG
Status	Released
Project	ENCODE3
ID	643

Experiment Information (Status: Released)

	BGHLV27-43	BGHLV27-44
idx	663	664
TRCN#_or_BGC#	TRCN0000049326	TRCN0000049326
shRNA_or_gRNA_sequence	GCAGTCTGATTCTAAAGGAAA	GCAGTCTGATTCTAAAGGAAA
PAM
Name	PPIG	PPIG
Sample_ID	BGHLV27-43	BGHLV27-44
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	PPIG	PPIG
qPCR_result	64.1	55.8
Ave_qPCR	59.9
RT-qPCR_primer-F	gtggagagctgattcccaaa
RT-qPCR_primer-R	tgaggaggaggaagatgatga
protein_conc	4962	4633
WB_result	83.1	87.4
Ave_WB	85.3
WB_DONE_date	7/27/2015
MW	89kDa
IP	1	1
antibody_Cat#	A302-075A	A302-075A
Antibody DCC ID	ENCAB460YIG	ENCAB460YIG
submitted_to_DCC_date	8/6/2015
Rep1_TPM	49	0
Rep2_TPM	31	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2750	2751

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PPIG	Product_ID: A302-075A Lot_ID: 1 Source: Bethyl Labs Target Name: PPIG-human

Experiment Status

	BGHLV27-43	BGHLV27-44
Sample_ID	BGHLV27-43	BGHLV27-44
Sample Name	PPIG_BGHLV27-43	PPIG_BGHLV27-44
Sample Name	PPIG_BGHLV27-43	PPIG_BGHLV27-44
RBP	PPIG	PPIG
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	972	973

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-43	BGHLV27-44
Sample #
Sample Name	PPIG-BGHLV27-43	PPIG-BGHLV27-44
Sample_Name_Alias	PPIG_BGHLV27-43	PPIG_BGHLV27-44
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/C2.png	DNA_Library_LV27/set1/D2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E5.png	RNA_Library_LV26-27-28-29/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-43	BGHLV27-44
RBP	PPIG	PPIG
Batch_ID	BGHLV27	BGHLV27
WB_result	83.100	87.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2664	2665

Sequencing Information

	BGHLV27-43	BGHLV27-44
Sample_ID	BGHLV27-43	BGHLV27-44
Sample Name	PPIG_BGHLV27-43	PPIG_BGHLV27-44
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	73,041,852	85,684,664
total_aligned_reads	67,502,818	78,810,270
unique_aligned_reads	63,654,450	74,252,560
percent_uniqueAligned	0.87148	0.86658
correlation_replicates	0.999051	0.999051
spikein_reads	275,512	317,706
percent_spikeins	0.00377	0.00371
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1306	1307

Data Submission Information

	BGHLV27-43	BGHLV27-43
ENCODE_alias	brenton-graveley:PPIG_BGHLV27	brenton-graveley:PPIG-BGHLV27-HepG2
ENCODE_accession	ENCSR620HAA	ENCSR692CHB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-43	BGHLV27-43
Sample Name	PPIG_BGHLV27-43	PPIG_BGHLV27-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3033	6862

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
PPIG_BGHLV27-43_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1306	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20018
PPIG_BGHLV27-43_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1306	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20040
PPIG_BGHLV27-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1306					GRCh38	V40	PPIG_BGHLV27-43_1.fastq.gz,PPIG_BGHLV27-43_2.fastq.gz		ENCORE2	20062
PPIG_BGHLV27-43_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1306					GRCh38	V40	PPIG_BGHLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	20084
PPIG_BGHLV27-43_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1306					GRCh38	V40	PPIG_BGHLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	20106
PPIG_BGHLV27-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1306					GRCh38	V40	PPIG_BGHLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	20128
PPIG_BGHLV27-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1306					GRCh38	V40	PPIG_BGHLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	20150
PPIG_BGHLV27-43_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1306					GRCh38	V40	PPIG_BGHLV27-43_1.fastq.gz,PPIG_BGHLV27-43_2.fastq.gz		ENCORE2	20690
PPIG_BGHLV27-44_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1307	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20019
PPIG_BGHLV27-44_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1307	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20041
PPIG_BGHLV27-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1307					GRCh38	V40	PPIG_BGHLV27-44_1.fastq.gz,PPIG_BGHLV27-44_2.fastq.gz		ENCORE2	20063
PPIG_BGHLV27-44_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1307					GRCh38	V40	PPIG_BGHLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	20085
PPIG_BGHLV27-44_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1307					GRCh38	V40	PPIG_BGHLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	20107
PPIG_BGHLV27-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1307					GRCh38	V40	PPIG_BGHLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	20129
PPIG_BGHLV27-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1307					GRCh38	V40	PPIG_BGHLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	20151
PPIG_BGHLV27-44_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1307					GRCh38	V40	PPIG_BGHLV27-44_1.fastq.gz,PPIG_BGHLV27-44_2.fastq.gz		ENCORE2	20691