GRWD1 RNA-Seq in HepG2

General Information


RBP	GRWD1
Cell_Line	HepG2
Method	shRNA
Exp_Name	GRWD1-BGHLV18-HepG2
ENCODE_series_ID	ENCSR677TMD
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR850FEH
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	GRWD1_BGHLV18_13
Rep2	GRWD1_BGHLV18_14
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	62.9
Rep2_qPCR	64.2
Rep1_WB	71.8
Rep2_WB	77.1
Antibody Cat#	A301-576A
Antibody Lot#	A301-576A
Antibody DCC ID	ENCAB573ZJV
Status	Released
Project	ENCODE3
ID	446

Experiment Information (Status: Released)

	BGHLV18-13	BGHLV18-14
idx	313	314
TRCN#_or_BGC#	TRCN0000135333	TRCN0000135333
shRNA_or_gRNA_sequence	CTCACCAAAGAACTCGGTTTA	CTCACCAAAGAACTCGGTTTA
PAM
Name	GRWD1	GRWD1
Sample_ID	BGHLV18-13	BGHLV18-14
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	GRWD1	GRWD1
qPCR_result	62.9	64.2
Ave_qPCR	63.5
RT-qPCR_primer-F	catcttctccttcgctggac
RT-qPCR_primer-R	ccagaggtggatgttcttttg
protein_conc	4330	4499
WB_result	71.8	77.1
Ave_WB	74.4
WB_DONE_date	2/17/2015
MW	49kDa
IP	1	1
antibody_Cat#	A301-576A	A301-576A
Antibody DCC ID	ENCAB573ZJV	ENCAB573ZJV
submitted_to_DCC_date	4/2/2015
Rep1_TPM	7.8	0
Rep2_TPM	8.3	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2378	2379

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GRWD1	Product_ID: A301-576A Lot_ID: 1 Source: Bethyl Labs Target Name: GRWD1-human

Experiment Status

	BGHLV18-13	BGHLV18-14
Sample_ID	BGHLV18-13	BGHLV18-14
Sample Name	GRWD1_BGHLV18_13	GRWD1_BGHLV18_14
Sample Name	GRWD1_BGHLV18_13	GRWD1_BGHLV18_14
RBP	GRWD1	GRWD1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	620	621

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-13	BGHLV18-14
Sample #
Sample Name	GRWD1-BGHLV18-13	GRWD1-BGHLV18-14
Sample_Name_Alias	GRWD1_BGHLV18_13	GRWD1_BGHLV18_14
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G1.png	DNA_Library_LV18-19/set1/H1.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E8.png	RNA_Library_LV16-17-18/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-13	BGHLV18-14
RBP	GRWD1	GRWD1
Batch_ID	BGHLV18	BGHLV18
WB_result	71.800	77.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2304	2305

Sequencing Information

	BGHLV18-13	BGHLV18-14
Sample_ID	BGHLV18-13	BGHLV18-14
Sample Name	GRWD1_BGHLV18_13	GRWD1_BGHLV18_14
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	44,030,000	46,680,000
total_aligned_reads	40,830,604	43,433,796
unique_aligned_reads	38,591,150	40,979,010
percent_uniqueAligned	0.87647	0.87787
correlation_replicates	0.991819	0.991819
spikein_reads	90,308	200,914
percent_spikeins	0.00205	0.00430
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	946	947

Data Submission Information

	BGHLV18-13	BGHLV18-13
ENCODE_alias	brenton-graveley:GRWD1_BGHLV18	brenton-graveley:GRWD1-BGHLV18-HepG2
ENCODE_accession	ENCSR850FEH	ENCSR677TMD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-13	BGHLV18-13
Sample Name	GRWD1_BGHLV18_13	GRWD1_BGHLV18_13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2827	6739

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
GRWD1_BGHLV18_13_CAGATC_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	946	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14794
GRWD1_BGHLV18_13_CAGATC_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	946	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14832
GRWD1_BGHLV18_13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	946					GRCh38	V40	GRWD1_BGHLV18_13_CAGATC_L008_R1_001.fastq.gz,GRWD1_BGHLV18_13_CAGATC_L008_R2_001.fastq.gz		ENCORE2	14870
GRWD1_BGHLV18_13_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	946					GRCh38	V40	GRWD1_BGHLV18_13/Aligned.sortedByCoord.out.bam		ENCORE2	14908
GRWD1_BGHLV18_13_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	946					GRCh38	V40	GRWD1_BGHLV18_13/Aligned.sortedByCoord.out.bam		ENCORE2	14946
GRWD1_BGHLV18_13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	946					GRCh38	V40	GRWD1_BGHLV18_13/Aligned.sortedByCoord.out.bam		ENCORE2	14984
GRWD1_BGHLV18_13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	946					GRCh38	V40	GRWD1_BGHLV18_13/Aligned.sortedByCoord.out.bam		ENCORE2	15022
GRWD1_BGHLV18_13_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	946					GRCh38	V40	GRWD1_BGHLV18_13_CAGATC_L008_R1_001.fastq.gz,GRWD1_BGHLV18_13_CAGATC_L008_R2_001.fastq.gz		ENCORE2	15060
GRWD1_BGHLV18_14_ACTTGA_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	947	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14795
GRWD1_BGHLV18_14_ACTTGA_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	947	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14833
GRWD1_BGHLV18_14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	947					GRCh38	V40	GRWD1_BGHLV18_14_ACTTGA_L008_R1_001.fastq.gz,GRWD1_BGHLV18_14_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	14871
GRWD1_BGHLV18_14_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	947					GRCh38	V40	GRWD1_BGHLV18_14/Aligned.sortedByCoord.out.bam		ENCORE2	14909
GRWD1_BGHLV18_14_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	947					GRCh38	V40	GRWD1_BGHLV18_14/Aligned.sortedByCoord.out.bam		ENCORE2	14947
GRWD1_BGHLV18_14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	947					GRCh38	V40	GRWD1_BGHLV18_14/Aligned.sortedByCoord.out.bam		ENCORE2	14985
GRWD1_BGHLV18_14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	947					GRCh38	V40	GRWD1_BGHLV18_14/Aligned.sortedByCoord.out.bam		ENCORE2	15023
GRWD1_BGHLV18_14_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	947					GRCh38	V40	GRWD1_BGHLV18_14_ACTTGA_L008_R1_001.fastq.gz,GRWD1_BGHLV18_14_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	15061