EIF4B RNA-Seq in HepG2

General Information


RBP	EIF4B
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF4B-BGHLV12-HepG2
ENCODE_series_ID	ENCSR113GLI
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR313CHR
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	EIF4B-BGHLV12-23
Rep2	EIF4B-BGHLV12-24
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	45.6
Rep2_qPCR	53.6
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A301-767A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB697PTS
Status	Archived
Project	ENCODE3
ID	336

Experiment Information (Status: Released)

	BGHLV12-23	BGHLV12-24
idx	23	24
TRCN#_or_BGC#	TRCN0000062598	TRCN0000062598
shRNA_or_gRNA_sequence	GCGGAGAAACACCTTGATCTT	GCGGAGAAACACCTTGATCTT
PAM
Name	EIF4B	EIF4B
Sample_ID	BGHLV12-23	BGHLV12-24
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	EIF4B	EIF4B
qPCR_result	45.6	53.6
Ave_qPCR	49.6
RT-qPCR_primer-F	AGCTCCAGCTCAACCATCTG
RT-qPCR_primer-R	AGAGTTCCCAGTTTGGCCTT
protein_conc	1644	525
WB_result	0.0	0.0
Ave_WB	0.0
WB_DONE_date	7/29/2015
MW	65kDa
IP	1	1
antibody_Cat#	A301-767A	A301-767A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	146.7	0
Rep2_TPM	129.7	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2070	2071

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV12-23	BGHLV12-24
Sample_ID	BGHLV12-23	BGHLV12-24
Sample Name	EIF4B-BGHLV12-23	EIF4B-BGHLV12-24
Sample Name	EIF4B-BGHLV12-23	EIF4B-BGHLV12-24
RBP	EIF4B	EIF4B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	386	387

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-23	BGHLV12-24
Sample #
Sample Name	EIF4B-BGHLV12-23	EIF4B-BGHLV12-24
Sample_Name_Alias	EIF4B-BGHLV12-23	EIF4B-BGHLV12-24
Index Well Position	S18	S19
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/set2/B1.png	DNA_Library_LV12/set2/C1.png
RIN	9.2	8.7
libSample_RNA_Well	RNA_Library_LV12/set1/A3.png	RNA_Library_LV12/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-23	BGHLV12-24
RBP	EIF4B	EIF4B
Batch_ID	BGHLV12	BGHLV12
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2008	2009

Sequencing Information

	BGHLV12-23	BGHLV12-24
Sample_ID	BGHLV12-23	BGHLV12-24
Sample Name	EIF4B-BGHLV12-23	EIF4B-BGHLV12-24
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	66,860,000	68,280,000
total_aligned_reads	63,087,644	64,511,266
unique_aligned_reads	59,309,030	60,601,594
percent_uniqueAligned	0.88706	0.88755
correlation_replicates	0.996201	0.996201
spikein_reads	434,408	940,342
percent_spikeins	0.00650	0.01377
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	708	709

Data Submission Information

	BGHLV12-23	BGHLV12-23
ENCODE_alias	brenton-graveley:EIF4B-BGHLV12	brenton-graveley:EIF4B-BGHLV12-HepG2
ENCODE_accession	ENCSR313CHR	ENCSR113GLI
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-23	BGHLV12-23
Sample Name	EIF4B-BGHLV12-23	EIF4B-BGHLV12-23
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2742	6691

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
EIF4B-BGHLV12-23_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	708	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12765
EIF4B-BGHLV12-23_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	708	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12834
EIF4B-BGHLV12-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	708					GRCh38	V40	EIF4B-BGHLV12-23_GTCCGC_L003_R1_001.fastq.gz,EIF4B-BGHLV12-23_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	12904
EIF4B-BGHLV12-23_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	708					GRCh38	V40	EIF4B-BGHLV12-23/Aligned.sortedByCoord.out.bam		ENCORE2	12974
EIF4B-BGHLV12-23_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	708					GRCh38	V40	EIF4B-BGHLV12-23/Aligned.sortedByCoord.out.bam		ENCORE2	13044
EIF4B-BGHLV12-23_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	708					GRCh38	V40	EIF4B-BGHLV12-23/Aligned.sortedByCoord.out.bam		ENCORE2	13114
EIF4B-BGHLV12-23_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	708					GRCh38	V40	EIF4B-BGHLV12-23/Aligned.sortedByCoord.out.bam		ENCORE2	13184
EIF4B-BGHLV12-23_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	708					GRCh38	V40	EIF4B-BGHLV12-23_GTCCGC_L003_R1_001.fastq.gz,EIF4B-BGHLV12-23_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	13254
EIF4B-BGHLV12-24_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	709	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12766
EIF4B-BGHLV12-24_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	709	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12835
EIF4B-BGHLV12-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	709					GRCh38	V40	EIF4B-BGHLV12-24_GTGAAA_L003_R1_001.fastq.gz,EIF4B-BGHLV12-24_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	12905
EIF4B-BGHLV12-24_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	709					GRCh38	V40	EIF4B-BGHLV12-24/Aligned.sortedByCoord.out.bam		ENCORE2	12975
EIF4B-BGHLV12-24_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	709					GRCh38	V40	EIF4B-BGHLV12-24/Aligned.sortedByCoord.out.bam		ENCORE2	13045
EIF4B-BGHLV12-24_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	709					GRCh38	V40	EIF4B-BGHLV12-24/Aligned.sortedByCoord.out.bam		ENCORE2	13115
EIF4B-BGHLV12-24_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	709					GRCh38	V40	EIF4B-BGHLV12-24/Aligned.sortedByCoord.out.bam		ENCORE2	13185
EIF4B-BGHLV12-24_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	709					GRCh38	V40	EIF4B-BGHLV12-24_GTGAAA_L003_R1_001.fastq.gz,EIF4B-BGHLV12-24_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	13255