EIF4A3 RNA-Seq in HepG2

General Information


RBP	EIF4A3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF4A3-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR676WWD
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR999MAE
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	EIF4A3-BGHcLV16-25
Rep2	EIF4A3-BGHcLV16-26
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	57.8
Rep2_qPCR	60.0
Rep1_WB	51.5
Rep2_WB	56.1
Antibody Cat#	PA5-54532
Antibody Lot#	LOT# TK2671524A
Antibody DCC ID	ENCAB214HYQ
Status	Released
Project	ENCODE4
ID	149

Experiment Information (Status: Released)

	BGHcLV16-25	BGHcLV16-26
idx	453	454
TRCN#_or_BGC#	BGC#0000347	BGC#0000347
shRNA_or_gRNA_sequence	GCCCATGGTGTCGAACGTGG	GCCCATGGTGTCGAACGTGG
PAM	GGG	GGG
Name	EIF4A3-94	EIF4A3-94
Sample_ID	BGHcLV16-25	BGHcLV16-26
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	EIF4A3	EIF4A3
qPCR_result	57.8	60.0
Ave_qPCR	58.9
RT-qPCR_primer-F	GAATTCGAGACCAGCGAGGA
RT-qPCR_primer-R	GCTGGATTGCTGATGGTTTT
protein_conc	3718	3738
WB_result	51.5	56.1
Ave_WB	53.8
WB_DONE_date	5/23/19
MW	58KD
IP	Mouse / Ig
antibody_Cat#	PA5-54532	LOT# TK2671524A
Antibody DCC ID	ENCAB214HYQ
submitted_to_DCC_date	4/17/19
Rep1_TPM	148	0
Rep2_TPM	129	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6602	6603

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4A3	Product_ID: PA5-54532 Lot_ID: TK2671524A Source: Thermo Fisher Target Name: EIF4A3-human

Experiment Status

	BGHcLV16-25	BGHcLV16-26
Sample_ID	BGHcLV16-25	BGHcLV16-26
Sample Name
Sample Name	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-26
RBP	EIF4A3	EIF4A3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5417	5418

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-25	BGHcLV16-26
Sample #	51	52
Sample Name	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-26
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	1-A2	1-B2
Tecan	22.43	35.26
Tecan_date	2019-12-10	2019-12-10
Size_bp	279	289
Peak_Molarity	37.10	28.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A2.png	DNA_Library_set43-44/set2/B2.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/A7.png	RNA_Library_set43-44/set1/B7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-25	BGHcLV16-26
RBP	EIF4A3	EIF4A3
Batch_ID	BGHcLV16	BGHcLV16
WB_result	51.500	56.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	627	628

Sequencing Information

	BGHcLV16-25	BGHcLV16-26
Sample_ID	BGHcLV16-25	BGHcLV16-26
Sample Name	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-26
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	110,022,450	119,171,554
total_aligned_reads	101,699,954	111,540,464
unique_aligned_reads	95,461,832	104,626,678
percent_uniqueAligned	0.86766	0.87795
correlation_replicates	0.996768	0.996768
spikein_reads	248,656	214,216
percent_spikeins	0.00226	0.00180
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	129	130

Data Submission Information

	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-26	BGHcLV16-26	BGHcLV16-26	BGHcLV16-26
ENCODE_alias	brenton-graveley:EIF4A3-BGHcLV16	brenton-graveley:EIF4A3-BGHcLV16-25	brenton-graveley:L-EIF4A3-BGHcLV16-25	brenton-graveley:EIF4A3-BGHcLV16-25_S47_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4A3-BGHcLV16-25_S47_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4A3-BGHcLV16-HepG2	brenton-graveley:EIF4A3-BGHcLV16-26	brenton-graveley:L-EIF4A3-BGHcLV16-26	brenton-graveley:EIF4A3-BGHcLV16-26_S48_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4A3-BGHcLV16-26_S48_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR999MAE	ENCBS338PVK	ENCLB000AGN	ENCFF818ONJ	ENCFF012VVL	ENCSR676WWD	ENCBS837RAQ	ENCLB728FZE	ENCFF790UHH	ENCFF782UNR
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	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-25	BGHcLV16-26	BGHcLV16-26	BGHcLV16-26	BGHcLV16-26
Sample Name	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-25	EIF4A3-BGHcLV16-26	EIF4A3-BGHcLV16-26	EIF4A3-BGHcLV16-26	EIF4A3-BGHcLV16-26
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		EIF4A3-BGHcLV16-25.pdf	L-EIF4A3-BGHcLV16-25.pdf				EIF4A3-BGHcLV16-26.pdf	L-EIF4A3-BGHcLV16-26.pdf
ID	5	92	256	422	454	7200	93	257	423	455

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-BGHcLV16-25_S47_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	129	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	7
EIF4A3-BGHcLV16-25_S47_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	129	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	39
EIF4A3-BGHcLV16-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	129					GRCh38	V40	EIF4A3-BGHcLV16-25_S47_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGHcLV16-25_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24170
EIF4A3-BGHcLV16-25_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	129					GRCh38	V40	EIF4A3-BGHcLV16-25/Aligned.sortedByCoord.out.bam		ENCORE2	24202
EIF4A3-BGHcLV16-25_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	129					GRCh38	V40	EIF4A3-BGHcLV16-25/Aligned.sortedByCoord.out.bam		ENCORE2	24234
EIF4A3-BGHcLV16-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	129					GRCh38	V40	EIF4A3-BGHcLV16-25/Aligned.sortedByCoord.out.bam		ENCORE2	24266
EIF4A3-BGHcLV16-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	129					GRCh38	V40	EIF4A3-BGHcLV16-25/Aligned.sortedByCoord.out.bam		ENCORE2	24298
EIF4A3-BGHcLV16-25_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	129					GRCh38	V40	EIF4A3-BGHcLV16-25_S47_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGHcLV16-25_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24330
EIF4A3-BGHcLV16-26_S48_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	130	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	8
EIF4A3-BGHcLV16-26_S48_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	130	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	40
EIF4A3-BGHcLV16-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	130					GRCh38	V40	EIF4A3-BGHcLV16-26_S48_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGHcLV16-26_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24171
EIF4A3-BGHcLV16-26_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	130					GRCh38	V40	EIF4A3-BGHcLV16-26/Aligned.sortedByCoord.out.bam		ENCORE2	24203
EIF4A3-BGHcLV16-26_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	130					GRCh38	V40	EIF4A3-BGHcLV16-26/Aligned.sortedByCoord.out.bam		ENCORE2	24235
EIF4A3-BGHcLV16-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	130					GRCh38	V40	EIF4A3-BGHcLV16-26/Aligned.sortedByCoord.out.bam		ENCORE2	24267
EIF4A3-BGHcLV16-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	130					GRCh38	V40	EIF4A3-BGHcLV16-26/Aligned.sortedByCoord.out.bam		ENCORE2	24299
EIF4A3-BGHcLV16-26_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	130					GRCh38	V40	EIF4A3-BGHcLV16-26_S48_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGHcLV16-26_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24331