EIF4A3 RNA-Seq in K562

General Information


RBP	EIF4A3
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF4A3-BGKcLV15-K562
ENCODE_series_ID	ENCSR635OQT
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR264MSX
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	EIF4A3-BGKcLV15-31
Rep2	EIF4A3-BGKcLV15-32
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	0.0
Rep2_qPCR	2.0
Rep1_WB	93.2
Rep2_WB	81.8
Antibody Cat#	PA5-54532
Antibody Lot#	LOT#TK2671524A
Antibody DCC ID	ENCAB214HYQ
Status	Released
Project	ENCODE4
ID	126

Experiment Information (Status: Released)

	BGKcLV15-31	BGKcLV15-32
idx	567	568
TRCN#_or_BGC#	BGC#0000348	BGC#0000348
shRNA_or_gRNA_sequence	CGAGCCCGAGGTCGCCATCG	CGAGCCCGAGGTCGCCATCG
PAM	TGG	TGG
Name	EIF4A3-94B	EIF4A3-94B
Sample_ID	BGKcLV15-31	BGKcLV15-32
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	EIF4A3	EIF4A3
qPCR_result	0.0	2.0
Ave_qPCR	1.0
RT-qPCR_primer-F	GAATTCGAGACCAGCGAGGA
RT-qPCR_primer-R	GCTGGATTGCTGATGGTTTT
protein_conc	4959	5415
WB_result	93.2	81.8
Ave_WB	87.5
WB_DONE_date	4/18/19
MW	47KD
IP	Rabbit / I
antibody_Cat#	PA5-54532	LOT#TK2671524A
Antibody DCC ID	ENCAB214HYQ
submitted_to_DCC_date	4/17/19
Rep1_TPM	89.1	0
Rep2_TPM	79.2	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4677	4678

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

	BGKcLV15-31	BGKcLV15-32
Sample_ID	BGKcLV15-31	BGKcLV15-32
Sample Name
Sample Name	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-32
RBP	EIF4A3	EIF4A3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5341	5342

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-31	BGKcLV15-32
Sample #	11	12
Sample Name	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-32
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	1-C2	1-D2
Tecan	30.98	41.47
Tecan_date	2019-12-10	2019-12-10
Size_bp	264	270
Peak_Molarity	19.50	24.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C2.png	DNA_Library_set43-44/set1/D2.png
RIN	9.3	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/C2.png	RNA_Library_set43-44/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-31	BGKcLV15-32
RBP	EIF4A3	EIF4A3
Batch_ID	BGKcLV15	BGKcLV15
WB_result	93.200	81.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	587	588

Sequencing Information

	BGKcLV15-31	BGKcLV15-32
Sample_ID	BGKcLV15-31	BGKcLV15-32
Sample Name	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-32
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	89,452,948	99,720,388
total_aligned_reads	81,430,376	93,668,598
unique_aligned_reads	74,276,912	85,350,028
percent_uniqueAligned	0.83035	0.85589
correlation_replicates	0.999521	0.999521
spikein_reads	57,918	93,472
percent_spikeins	0.00065	0.00094
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	93	94

Data Submission Information

	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-32	BGKcLV15-32	BGKcLV15-32	BGKcLV15-32
ENCODE_alias	brenton-graveley:EIF4A3-BGKcLV15	brenton-graveley:EIF4A3-BGKcLV15-31	brenton-graveley:L-EIF4A3-BGKcLV15-31	brenton-graveley:EIF4A3-BGKcLV15-31_S11_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4A3-BGKcLV15-31_S11_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4A3-BGKcLV15-K562	brenton-graveley:EIF4A3-BGKcLV15-32	brenton-graveley:L-EIF4A3-BGKcLV15-32	brenton-graveley:EIF4A3-BGKcLV15-32_S12_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4A3-BGKcLV15-32_S12_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR264MSX	ENCBS439XGT	ENCLB452ZRI	ENCFF235JMU	ENCFF252FBR	ENCSR635OQT	ENCBS189BWL	ENCLB186YBO	ENCFF946PNM	ENCFF277CAQ
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	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-31	BGKcLV15-32	BGKcLV15-32	BGKcLV15-32	BGKcLV15-32
Sample Name	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-31	EIF4A3-BGKcLV15-32	EIF4A3-BGKcLV15-32	EIF4A3-BGKcLV15-32	EIF4A3-BGKcLV15-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		EIF4A3-BGKcLV15-31.pdf	L-EIF4A3-BGKcLV15-31.pdf				EIF4A3-BGKcLV15-32.pdf	L-EIF4A3-BGKcLV15-32.pdf
ID	22	126	290	488	540	7201	127	291	489	541

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-BGKcLV15-31_S11_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	93	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	85
EIF4A3-BGKcLV15-31_S11_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	93	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	137
EIF4A3-BGKcLV15-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	93					GRCh38	V40	EIF4A3-BGKcLV15-31_S11_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGKcLV15-31_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24376
EIF4A3-BGKcLV15-31_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	93					GRCh38	V40	EIF4A3-BGKcLV15-31/Aligned.sortedByCoord.out.bam		ENCORE2	24428
EIF4A3-BGKcLV15-31_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	93					GRCh38	V40	EIF4A3-BGKcLV15-31/Aligned.sortedByCoord.out.bam		ENCORE2	24480
EIF4A3-BGKcLV15-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	93					GRCh38	V40	EIF4A3-BGKcLV15-31/Aligned.sortedByCoord.out.bam		ENCORE2	24532
EIF4A3-BGKcLV15-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	93					GRCh38	V40	EIF4A3-BGKcLV15-31/Aligned.sortedByCoord.out.bam		ENCORE2	24584
EIF4A3-BGKcLV15-31_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	93					GRCh38	V40	EIF4A3-BGKcLV15-31_S11_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGKcLV15-31_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24636
EIF4A3-BGKcLV15-32_S12_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	94	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	86
EIF4A3-BGKcLV15-32_S12_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	94	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	138
EIF4A3-BGKcLV15-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	94					GRCh38	V40	EIF4A3-BGKcLV15-32_S12_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGKcLV15-32_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24377
EIF4A3-BGKcLV15-32_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	94					GRCh38	V40	EIF4A3-BGKcLV15-32/Aligned.sortedByCoord.out.bam		ENCORE2	24429
EIF4A3-BGKcLV15-32_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	94					GRCh38	V40	EIF4A3-BGKcLV15-32/Aligned.sortedByCoord.out.bam		ENCORE2	24481
EIF4A3-BGKcLV15-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	94					GRCh38	V40	EIF4A3-BGKcLV15-32/Aligned.sortedByCoord.out.bam		ENCORE2	24533
EIF4A3-BGKcLV15-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	94					GRCh38	V40	EIF4A3-BGKcLV15-32/Aligned.sortedByCoord.out.bam		ENCORE2	24585
EIF4A3-BGKcLV15-32_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	94					GRCh38	V40	EIF4A3-BGKcLV15-32_S12_R1_001.filtered.trimmed.paired.fastq.gz,EIF4A3-BGKcLV15-32_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24637