EIF4B RNA-Seq in HepG2

General Information


RBP	EIF4B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF4B-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR384VJF
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR323OPW
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	EIF4B-BGHcLV10-23
Rep2	EIF4B-BGHcLV10-24
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	59.8
Rep2_qPCR	75.1
Rep1_WB	94.5
Rep2_WB	99.2
Antibody Cat#	A301-767A
Antibody Lot#	A301-767A
Antibody DCC ID	ENCAB697PTS
Status	Released
Project	ENCODE4
ID	223

Experiment Information (Status: Released)

	BGHcLV10-23	BGHcLV10-24
idx	220	221
TRCN#_or_BGC#	BGC#0000118	BGC#0000118
shRNA_or_gRNA_sequence	GTCATCGTTACTGTGCCAAG	GTCATCGTTACTGTGCCAAG
PAM	TGG	TGG
Name	EIF4B-87	EIF4B-87
Sample_ID	BGHcLV10-23	BGHcLV10-24
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	EIF4B	EIF4B
qPCR_result	59.8	75.1
Ave_qPCR	67.5
RT-qPCR_primer-F	AGCTCCAGCTCAACCATCTG
RT-qPCR_primer-R	AGAGTTCCCAGTTTGGCCTT
protein_conc	1869	2559
WB_result	94.5	99.2
Ave_WB	96.9
WB_DONE_date	5/10/18	wes
MW	65kDa
IP	1	1
antibody_Cat#	A301-767A	A301-767A
Antibody DCC ID	ENCAB697PTS
submitted_to_DCC_date	9/6/18
Rep1_TPM	364	0
Rep2_TPM	389	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6363	6364

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4B	Product_ID: A301-767A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF4B-human

Experiment Status

	BGHcLV10-23	BGHcLV10-24
Sample_ID	BGHcLV10-23	BGHcLV10-24
Sample Name
Sample Name	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-24
RBP	EIF4B	EIF4B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6297	6298

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-23	BGHcLV10-24
Sample #	57	58
Sample Name	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-24
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	272	272
Peak_Molarity	65.00	32.10
libSampleQC_DNA_Well	DNA_Library_set41/set5/E8.png	DNA_Library_set41/set5/F8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set41/set1/A8.png	RNA_Library_set41/set1/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-23	BGHcLV10-24
RBP	EIF4B	EIF4B
Batch_ID	BGHcLV10	BGHcLV10
WB_result	94.500	99.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	907	908

Sequencing Information

	BGHcLV10-23	BGHcLV10-24
Sample_ID	BGHcLV10-23	BGHcLV10-24
Sample Name	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-24
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	94,508,304	198,507,346
total_aligned_reads	90,516,526	189,864,180
unique_aligned_reads	84,228,150	176,616,714
percent_uniqueAligned	0.89122	0.88972
correlation_replicates	0.992822	0.992822
spikein_reads	175,336	326,648
percent_spikeins	0.00186	0.00165
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	313	314

Data Submission Information

	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-24	BGHcLV10-24	BGHcLV10-24	BGHcLV10-24
ENCODE_alias	brenton-graveley:EIF4B-BGHcLV10	brenton-graveley:EIF4B-BGHcLV10-23	brenton-graveley:L-EIF4B-BGHcLV10-23	brenton-graveley:EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4B-BGHcLV10-HepG2	brenton-graveley:EIF4B-BGHcLV10-24	brenton-graveley:L-EIF4B-BGHcLV10-24	brenton-graveley:EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR323OPW	ENCBS869XGC	ENCLB395PDQ	ENCFF654BZD	ENCFF954FQB	ENCSR384VJF	ENCBS710LUH	ENCLB776BXV	ENCFF837GDY	ENCFF809FUF
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-23	BGHcLV10-24	BGHcLV10-24	BGHcLV10-24	BGHcLV10-24
Sample Name	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-23	EIF4B-BGHcLV10-24	EIF4B-BGHcLV10-24	EIF4B-BGHcLV10-24	EIF4B-BGHcLV10-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		EIF4B-BGHcLV10-23.pdf	L-EIF4B-BGHcLV10-23.pdf				EIF4B-BGHcLV10-24.pdf	L-EIF4B-BGHcLV10-24.pdf
ID	1125	1170	1240	1310	1380	7202	1171	1241	1311	1381

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	313				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	517
EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	313				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	587
EIF4B-BGHcLV10-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	313	GRCh38	V40	EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26755
EIF4B-BGHcLV10-23_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	313	GRCh38	V40	EIF4B-BGHcLV10-23/Aligned.sortedByCoord.out.bam		ENCORE2	26825
EIF4B-BGHcLV10-23_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	313	GRCh38	V40	EIF4B-BGHcLV10-23/Aligned.sortedByCoord.out.bam		ENCORE2	26895
EIF4B-BGHcLV10-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	313	GRCh38	V40	EIF4B-BGHcLV10-23/Aligned.sortedByCoord.out.bam		ENCORE2	26965
EIF4B-BGHcLV10-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	313	GRCh38	V40	EIF4B-BGHcLV10-23/Aligned.sortedByCoord.out.bam		ENCORE2	27035
EIF4B-BGHcLV10-23_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	313	GRCh38	V40	EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGHcLV10-23_CGGAACTG+CACTACGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27105
EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	314				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	518
EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	314				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	588
EIF4B-BGHcLV10-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	314	GRCh38	V40	EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26756
EIF4B-BGHcLV10-24_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	314	GRCh38	V40	EIF4B-BGHcLV10-24/Aligned.sortedByCoord.out.bam		ENCORE2	26826
EIF4B-BGHcLV10-24_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	314	GRCh38	V40	EIF4B-BGHcLV10-24/Aligned.sortedByCoord.out.bam		ENCORE2	26896
EIF4B-BGHcLV10-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	314	GRCh38	V40	EIF4B-BGHcLV10-24/Aligned.sortedByCoord.out.bam		ENCORE2	26966
EIF4B-BGHcLV10-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	314	GRCh38	V40	EIF4B-BGHcLV10-24/Aligned.sortedByCoord.out.bam		ENCORE2	27036
EIF4B-BGHcLV10-24_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	314	GRCh38	V40	EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGHcLV10-24_TAAGGTCA+TGTCGTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27106