RACK1 RNA-Seq in HepG2

General Information


RBP	GNB2L1
Cell_Line	HepG2
Method	shRNA
Exp_Name	GNB2L1-BGHLV18-HepG2
ENCODE_series_ID	ENCSR699MDT
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR116YMU
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	GNB2L1_BGHLV18_11
Rep2	GNB2L1_BGHLV18_12
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	78.7
Rep2_qPCR	86.5
Rep1_WB	41.0
Rep2_WB	46.3
Antibody Cat#	A302-545A
Antibody Lot#	A302-545A
Antibody DCC ID	ENCAB611SPG
Status	Released
Project	ENCODE3
ID	445

Experiment Information (Status: Released)

	BGHLV18-11	BGHLV18-12
idx	311	312
TRCN#_or_BGC#	TRCN0000006472	TRCN0000006472
shRNA_or_gRNA_sequence	GATGTGGTTATCTCCTCAGAT	GATGTGGTTATCTCCTCAGAT
PAM
Name	GNB2L1	GNB2L1
Sample_ID	BGHLV18-11	BGHLV18-12
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	GNB2L1	GNB2L1
qPCR_result	78.7	86.5
Ave_qPCR	82.6
RT-qPCR_primer-F	atcgctactaccccgcagtt
RT-qPCR_primer-R	atccctggtcagtttccaca
protein_conc	4365	3871
WB_result	41.0	46.3
Ave_WB	43.6
WB_DONE_date	3/27/2015
MW	35kDa
IP	1	1
antibody_Cat#	A302-545A	A302-545A
Antibody DCC ID	ENCAB611SPG	ENCAB611SPG
submitted_to_DCC_date	5/4/2015
Rep1_TPM	1316.1	0
Rep2_TPM	1492.7	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2376	2377

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GNB2L1	Product_ID: A302-545A Lot_ID: 1 Source: Bethyl Labs Target Name: GNB2L1-human

Experiment Status

	BGHLV18-11	BGHLV18-12
Sample_ID	BGHLV18-11	BGHLV18-12
Sample Name	GNB2L1_BGHLV18_11	GNB2L1_BGHLV18_12
Sample Name	GNB2L1_BGHLV18_11	GNB2L1_BGHLV18_12
RBP	GNB2L1	GNB2L1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	618	619

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-11	BGHLV18-12
Sample #
Sample Name	GNB2L1-BGHLV18-11	GNB2L1-BGHLV18-12
Sample_Name_Alias	GNB2L1_BGHLV18_11	GNB2L1_BGHLV18_12
Index Well Position	S05	S06
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/E1.png	DNA_Library_LV18-19/set1/F1.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C8.png	RNA_Library_LV16-17-18/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-11	BGHLV18-12
RBP	GNB2L1	GNB2L1
Batch_ID	BGHLV18	BGHLV18
WB_result	41.000	46.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2302	2303

Sequencing Information

	BGHLV18-11	BGHLV18-12
Sample_ID	BGHLV18-11	BGHLV18-12
Sample Name	GNB2L1_BGHLV18_11	GNB2L1_BGHLV18_12
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	38,680,000	59,800,000
total_aligned_reads	35,702,964	55,489,138
unique_aligned_reads	33,689,326	52,413,968
percent_uniqueAligned	0.87098	0.87649
correlation_replicates	0.983313	0.983313
spikein_reads	108,308	153,184
percent_spikeins	0.00280	0.00256
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	944	945

Data Submission Information

	BGHLV18-11	BGHLV18-11
ENCODE_alias	brenton-graveley:GNB2L1_BGHLV18	brenton-graveley:GNB2L1-BGHLV18-HepG2
ENCODE_accession	ENCSR116YMU	ENCSR699MDT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-11	BGHLV18-11
Sample Name	GNB2L1_BGHLV18_11	GNB2L1_BGHLV18_11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2826	6734

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
GNB2L1_BGHLV18_11_ACAGTG_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	944	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14792
GNB2L1_BGHLV18_11_ACAGTG_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	944	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14830
GNB2L1_BGHLV18_11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	944					GRCh38	V40	GNB2L1_BGHLV18_11_ACAGTG_L008_R1_001.fastq.gz,GNB2L1_BGHLV18_11_ACAGTG_L008_R2_001.fastq.gz		ENCORE2	14868
GNB2L1_BGHLV18_11_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	944					GRCh38	V40	GNB2L1_BGHLV18_11/Aligned.sortedByCoord.out.bam		ENCORE2	14906
GNB2L1_BGHLV18_11_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	944					GRCh38	V40	GNB2L1_BGHLV18_11/Aligned.sortedByCoord.out.bam		ENCORE2	14944
GNB2L1_BGHLV18_11_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	944					GRCh38	V40	GNB2L1_BGHLV18_11/Aligned.sortedByCoord.out.bam		ENCORE2	14982
GNB2L1_BGHLV18_11_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	944					GRCh38	V40	GNB2L1_BGHLV18_11/Aligned.sortedByCoord.out.bam		ENCORE2	15020
GNB2L1_BGHLV18_11_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	944					GRCh38	V40	GNB2L1_BGHLV18_11_ACAGTG_L008_R1_001.fastq.gz,GNB2L1_BGHLV18_11_ACAGTG_L008_R2_001.fastq.gz		ENCORE2	15058
GNB2L1_BGHLV18_12_GCCAAT_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	945	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14793
GNB2L1_BGHLV18_12_GCCAAT_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	945	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14831
GNB2L1_BGHLV18_12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	945					GRCh38	V40	GNB2L1_BGHLV18_12_GCCAAT_L008_R1_001.fastq.gz,GNB2L1_BGHLV18_12_GCCAAT_L008_R2_001.fastq.gz		ENCORE2	14869
GNB2L1_BGHLV18_12_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	945					GRCh38	V40	GNB2L1_BGHLV18_12/Aligned.sortedByCoord.out.bam		ENCORE2	14907
GNB2L1_BGHLV18_12_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	945					GRCh38	V40	GNB2L1_BGHLV18_12/Aligned.sortedByCoord.out.bam		ENCORE2	14945
GNB2L1_BGHLV18_12_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	945					GRCh38	V40	GNB2L1_BGHLV18_12/Aligned.sortedByCoord.out.bam		ENCORE2	14983
GNB2L1_BGHLV18_12_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	945					GRCh38	V40	GNB2L1_BGHLV18_12/Aligned.sortedByCoord.out.bam		ENCORE2	15021
GNB2L1_BGHLV18_12_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	945					GRCh38	V40	GNB2L1_BGHLV18_12_GCCAAT_L008_R1_001.fastq.gz,GNB2L1_BGHLV18_12_GCCAAT_L008_R2_001.fastq.gz		ENCORE2	15059