HDGF RNA-Seq in HepG2

General Information


RBP	HDGF
Cell_Line	HepG2
Method	shRNA
Exp_Name	HDGF-BGHLV31-HepG2
ENCODE_series_ID	ENCSR099YOB
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR634KHL
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	HDGF_BGHLV31-39
Rep2	HDGF_BGHLV31-40
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	94.4
Rep2_qPCR	95.0
Rep1_WB	86.3
Rep2_WB	87.2
Antibody Cat#	A303-170A
Antibody Lot#	A303-170A
Antibody DCC ID	ENCAB173GGB
Status	Released
Project	ENCODE3
ID	697

Experiment Information (Status: Released)

	BGHLV31-39	BGHLV31-40
idx	787	788
TRCN#_or_BGC#	TRCN0000118159	TRCN0000118159
shRNA_or_gRNA_sequence	GAACGAGAAAGGAGCGTTGAA	GAACGAGAAAGGAGCGTTGAA
PAM
Name	HDGF	HDGF
Sample_ID	BGHLV31-39	BGHLV31-40
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	HDGF	HDGF
qPCR_result	94.4	95.0
Ave_qPCR	94.7
RT-qPCR_primer-F	cctccccaagaggaagaaga	cctccccaagaggaagaaga
RT-qPCR_primer-R	cattggtggctacaggctct	cattggtggctacaggctct
protein_conc	4380	4519
WB_result	86.3	87.2
Ave_WB	86.8
WB_DONE_date	12/3/2015
MW	27kDa
IP	1MW	1MW
antibody_Cat#	A303-170A	A303-170A
Antibody DCC ID	ENCAB173GGB	ENCAB173GGB
submitted_to_DCC_date	12/7/2015
Rep1_TPM	33.3	0
Rep2_TPM	25.7	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2876	2877

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HDGF	Product_ID: A303-170A Lot_ID: 1 Source: Bethyl Labs Target Name: HDGF-human

Experiment Status

	BGHLV31-39	BGHLV31-40
Sample_ID	BGHLV31-39	BGHLV31-40
Sample Name	HDGF_BGHLV31-39	HDGF_BGHLV31-40
Sample Name	HDGF_BGHLV31-39	HDGF_BGHLV31-40
RBP	HDGF	HDGF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1121	1122

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-39	BGHLV31-40
Sample #
Sample Name	HDGF-BGHLV31-39	HDGF-BGHLV31-40
Sample_Name_Alias	HDGF_BGHLV31-39	HDGF_BGHLV31-40
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/G6.png	DNA_Library_LV31-21B/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G9.png	RNA_Library_LV29-30-31-32/set1/H9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-39	BGHLV31-40
RBP	HDGF	HDGF
Batch_ID	BGHLV31	BGHLV31
WB_result	86.300	87.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2818	2819

Sequencing Information

	BGHLV31-39	BGHLV31-40
Sample_ID	BGHLV31-39	BGHLV31-40
Sample Name	HDGF_BGHLV31-39	HDGF_BGHLV31-40
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	54,930,144	61,549,964
total_aligned_reads	49,814,684	56,184,904
unique_aligned_reads	47,004,036	53,075,274
percent_uniqueAligned	0.85571	0.86231
correlation_replicates	0.997736	0.997736
spikein_reads	245,198	280,114
percent_spikeins	0.00446	0.00455
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1467	1468

Data Submission Information

	BGHLV31-39	BGHLV31-39
ENCODE_alias	brenton-graveley:HDGF_BGHLV31	brenton-graveley:HDGF-BGHLV31-HepG2
ENCODE_accession	ENCSR634KHL	ENCSR099YOB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-39	BGHLV31-39
Sample Name	HDGF_BGHLV31-39	HDGF_BGHLV31-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3093	6743

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
HDGF_BGHLV31-39_ACTGAT_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1467	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20982
HDGF_BGHLV31-39_ACTGAT_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1467	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21008
HDGF_BGHLV31-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1467					GRCh38	V40	HDGF_BGHLV31-39_ACTGAT_L006_001.R1.fastq.gz,HDGF_BGHLV31-39_ACTGAT_L006_001.R2.fastq.gz		ENCORE2	21042
HDGF_BGHLV31-39_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1467					GRCh38	V40	HDGF_BGHLV31-39/Aligned.sortedByCoord.out.bam		ENCORE2	21068
HDGF_BGHLV31-39_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1467					GRCh38	V40	HDGF_BGHLV31-39/Aligned.sortedByCoord.out.bam		ENCORE2	21094
HDGF_BGHLV31-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1467					GRCh38	V40	HDGF_BGHLV31-39/Aligned.sortedByCoord.out.bam		ENCORE2	21120
HDGF_BGHLV31-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1467					GRCh38	V40	HDGF_BGHLV31-39/Aligned.sortedByCoord.out.bam		ENCORE2	21146
HDGF_BGHLV31-39_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1467					GRCh38	V40	HDGF_BGHLV31-39_ACTGAT_L006_001.R1.fastq.gz,HDGF_BGHLV31-39_ACTGAT_L006_001.R2.fastq.gz		ENCORE2	21172
HDGF_BGHLV31-40_ATTCCT_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1468	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20983
HDGF_BGHLV31-40_ATTCCT_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1468	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21009
HDGF_BGHLV31-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1468					GRCh38	V40	HDGF_BGHLV31-40_ATTCCT_L006_001.R1.fastq.gz,HDGF_BGHLV31-40_ATTCCT_L006_001.R2.fastq.gz		ENCORE2	21043
HDGF_BGHLV31-40_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1468					GRCh38	V40	HDGF_BGHLV31-40/Aligned.sortedByCoord.out.bam		ENCORE2	21069
HDGF_BGHLV31-40_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1468					GRCh38	V40	HDGF_BGHLV31-40/Aligned.sortedByCoord.out.bam		ENCORE2	21095
HDGF_BGHLV31-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1468					GRCh38	V40	HDGF_BGHLV31-40/Aligned.sortedByCoord.out.bam		ENCORE2	21121
HDGF_BGHLV31-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1468					GRCh38	V40	HDGF_BGHLV31-40/Aligned.sortedByCoord.out.bam		ENCORE2	21147
HDGF_BGHLV31-40_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1468					GRCh38	V40	HDGF_BGHLV31-40_ATTCCT_L006_001.R1.fastq.gz,HDGF_BGHLV31-40_ATTCCT_L006_001.R2.fastq.gz		ENCORE2	21173