EIF4A3 RNA-Seq in HepG2

General Information


RBP	EIF4A3
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF4A3-BGHLV12-HepG2
ENCODE_series_ID	ENCSR263EJV
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR957EEG
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	EIF4A3-BGHLV12-21
Rep2	EIF4A3-BGHLV12-22
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	43.2
Rep2_qPCR	44.9
Rep1_WB	71.9
Rep2_WB	63.4
Antibody Cat#	A302-981A
Antibody Lot#	A302-981A
Antibody DCC ID	ENCAB574DGT
Status	Released
Project	ENCODE3
ID	335

Experiment Information (Status: Released)

	BGHLV12-21	BGHLV12-22
idx	21	22
TRCN#_or_BGC#	TRCN0000061855	TRCN0000061855
shRNA_or_gRNA_sequence	GCAATCAAGCAGATCATCAAA	GCAATCAAGCAGATCATCAAA
PAM
Name	EIF4A3	EIF4A3
Sample_ID	BGHLV12-21	BGHLV12-22
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	EIF4A3	EIF4A3
qPCR_result	43.2	44.9
Ave_qPCR	44.1
RT-qPCR_primer-F	CATCCGCATCCTCAGAGATA
RT-qPCR_primer-R	CCCACTGATCTGCTGCTTC
protein_conc	1971	644
WB_result	71.9	63.4
Ave_WB	67.7
WB_DONE_date
MW	47kDa
IP	1	1
antibody_Cat#	A302-981A	A302-981A
Antibody DCC ID	ENCAB574DGT	ENCAB574DGT
submitted_to_DCC_date	4/2/2015
Rep1_TPM	54.2	0
Rep2_TPM	59.2	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2068	2069

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4A3	Product_ID: A302-981A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF4A3-human

Experiment Status

	BGHLV12-21	BGHLV12-22
Sample_ID	BGHLV12-21	BGHLV12-22
Sample Name	EIF4A3-BGHLV12-21	EIF4A3-BGHLV12-22
Sample Name	EIF4A3-BGHLV12-21	EIF4A3-BGHLV12-22
RBP	EIF4A3	EIF4A3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	384	385

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-21	BGHLV12-22
Sample #
Sample Name	EIF4A3-BGHLV12-21	EIF4A3-BGHLV12-22
Sample_Name_Alias	EIF4A3-BGHLV12-21	EIF4A3-BGHLV12-22
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set1/G2.png	DNA_Library_LV12/set2/A1.png
RIN	9.1	7.7
libSample_RNA_Well	RNA_Library_LV12/set1/G2.png	RNA_Library_LV12/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-21	BGHLV12-22
RBP	EIF4A3	EIF4A3
Batch_ID	BGHLV12	BGHLV12
WB_result	71.900	63.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2006	2007

Sequencing Information

	BGHLV12-21	BGHLV12-22
Sample_ID	BGHLV12-21	BGHLV12-22
Sample Name	EIF4A3-BGHLV12-21	EIF4A3-BGHLV12-22
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	78,660,000	64,180,000
total_aligned_reads	73,523,732	59,734,520
unique_aligned_reads	69,691,772	56,643,880
percent_uniqueAligned	0.88599	0.88258
correlation_replicates	0.998157	0.998157
spikein_reads	659,172	615,060
percent_spikeins	0.00838	0.00958
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	706	707

Data Submission Information

	BGHLV12-21	BGHLV12-21
ENCODE_alias	brenton-graveley:EIF4A3-BGHLV12	brenton-graveley:EIF4A3-BGHLV12-HepG2
ENCODE_accession	ENCSR957EEG	ENCSR263EJV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-21	BGHLV12-21
Sample Name	EIF4A3-BGHLV12-21	EIF4A3-BGHLV12-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2741	6689

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
EIF4A3-BGHLV12-21_ATGTCA_L003_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	706	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12763
EIF4A3-BGHLV12-21_ATGTCA_L003_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	706	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12832
EIF4A3-BGHLV12-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	706					GRCh38	V40	EIF4A3-BGHLV12-21_ATGTCA_L003_R1_001.fastq.gz,EIF4A3-BGHLV12-21_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	12902
EIF4A3-BGHLV12-21_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	706					GRCh38	V40	EIF4A3-BGHLV12-21/Aligned.sortedByCoord.out.bam		ENCORE2	12972
EIF4A3-BGHLV12-21_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	706					GRCh38	V40	EIF4A3-BGHLV12-21/Aligned.sortedByCoord.out.bam		ENCORE2	13042
EIF4A3-BGHLV12-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	706					GRCh38	V40	EIF4A3-BGHLV12-21/Aligned.sortedByCoord.out.bam		ENCORE2	13112
EIF4A3-BGHLV12-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	706					GRCh38	V40	EIF4A3-BGHLV12-21/Aligned.sortedByCoord.out.bam		ENCORE2	13182
EIF4A3-BGHLV12-21_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	706					GRCh38	V40	EIF4A3-BGHLV12-21_ATGTCA_L003_R1_001.fastq.gz,EIF4A3-BGHLV12-21_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	13252
EIF4A3-BGHLV12-22_CCGTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	707	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12764
EIF4A3-BGHLV12-22_CCGTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	707	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12833
EIF4A3-BGHLV12-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	707					GRCh38	V40	EIF4A3-BGHLV12-22_CCGTCC_L003_R1_001.fastq.gz,EIF4A3-BGHLV12-22_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	12903
EIF4A3-BGHLV12-22_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	707					GRCh38	V40	EIF4A3-BGHLV12-22/Aligned.sortedByCoord.out.bam		ENCORE2	12973
EIF4A3-BGHLV12-22_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	707					GRCh38	V40	EIF4A3-BGHLV12-22/Aligned.sortedByCoord.out.bam		ENCORE2	13043
EIF4A3-BGHLV12-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	707					GRCh38	V40	EIF4A3-BGHLV12-22/Aligned.sortedByCoord.out.bam		ENCORE2	13113
EIF4A3-BGHLV12-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	707					GRCh38	V40	EIF4A3-BGHLV12-22/Aligned.sortedByCoord.out.bam		ENCORE2	13183
EIF4A3-BGHLV12-22_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	707					GRCh38	V40	EIF4A3-BGHLV12-22_CCGTCC_L003_R1_001.fastq.gz,EIF4A3-BGHLV12-22_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	13253