EIF4G1 RNA-Seq in K562

General Information


RBP	EIF4G1
Cell_Line	K562
Method	shRNA
Exp_Name	EIF4G1-BGKLV24-K562
ENCODE_series_ID	ENCSR006GDY
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR712CSN
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	EIF4G1_BGKLV24_25_17615
Rep2	EIF4G1_BGKLV24_26_17616
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	86.2
Rep2_qPCR	81.3
Rep1_WB	91.4
Rep2_WB	90.1
Antibody Cat#	RN002P
Antibody Lot#	RN002P
Antibody DCC ID	ENCAB000BFI
Status	Released
Project	ENCODE3
ID	564

Experiment Information (Status: Released)

	BGKLV24-25	BGKLV24-25	BGKLV24-26	BGKLV24-26
idx	362	362	363	363
TRCN#_or_BGC#	TRCN0000061769	TRCN0000061769	TRCN0000061769	TRCN0000061769
shRNA_or_gRNA_sequence	GCCCTTGTAGTGACCTTAGAA	GCCCTTGTAGTGACCTTAGAA	GCCCTTGTAGTGACCTTAGAA	GCCCTTGTAGTGACCTTAGAA
PAM
Name	EIF4G1_69	EIF4G1_69	EIF4G1_69	EIF4G1_69
Sample_ID	BGKLV24-25	BGKLV24-25	BGKLV24-26	BGKLV24-26
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	EIF4G1	EIF4G1	EIF4G1	EIF4G1
qPCR_result	86.2	86.2	81.3	81.3
Ave_qPCR	83.8	83.8
RT-qPCR_primer-F	caacctgagtgagcagcaga	caacctgagtgagcagcaga
RT-qPCR_primer-R	cggaggggagtctcaaaaat	cggaggggagtctcaaaaat
protein_conc	3032	3032	3633	3633
WB_result	91.4	77.5	90.1	88.0
Ave_WB	90.8	82.8
WB_DONE_date	3/9/2015	7/9/10
MW
IP	1		1
antibody_Cat#	RN002P	MA5-14971	RN002P	LOT# TL2693034
Antibody DCC ID	ENCAB000BFI	ENCAB974ESP	ENCAB000BFI
submitted_to_DCC_date	5/4/2015
Rep1_TPM	174.203398	0	0	0
Rep2_TPM	100.217732	0	0	0
Action
Library_start_date	5/22/2015		5/22/2015
repeat_library
Note
ID	415	417	416	418

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4G1	Product_ID: RN002P Lot_ID: 2 Source: MBLI Target Name: EIF4G1-human
EIF4G1	Product_ID: MA5-14971 Lot_ID: TL2693034 Source: Thermo Fisher Target Name: EIF4G1-human

Experiment Status

	BGKLV24-25	BGKLV24-26
Sample_ID	BGKLV24-25	BGKLV24-26
Sample Name	EIF4G1_BGKLV24_25_17615	EIF4G1_BGKLV24_26_17616
Sample Name	EIF4G1_BGKLV24_25_17615	EIF4G1_BGKLV24_26_17616
RBP	EIF4G1	EIF4G1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	866	867

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-25	BGKLV24-26
Sample #
Sample Name	EIF4G1-BGKLV24-25	EIF4G1-BGKLV24-26
Sample_Name_Alias	EIF4G1_BGKLV24_25_17615	EIF4G1_BGKLV24_26_17616
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/E3.png	DNA_Library_LV21-24/set1/F3.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/B3.png	RNA_Library_LV20-22-24/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-25	BGKLV24-26
RBP	EIF4G1	EIF4G1
Batch_ID	BGKLV24	BGKLV24
WB_result	91.400	90.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2554	2555

Sequencing Information

	BGKLV24-25	BGKLV24-26
Sample_ID	BGKLV24-25	BGKLV24-26
Sample Name	EIF4G1_BGKLV24_25_17615	EIF4G1_BGKLV24_26_17616
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	38,250,000	41,770,000
total_aligned_reads	36,060,632	39,404,094
unique_aligned_reads	33,022,036	35,998,912
percent_uniqueAligned	0.86332	0.86184
correlation_replicates	0.979161	0.979161
spikein_reads	177,020	160,900
percent_spikeins	0.00463	0.00385
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1088	1089

Data Submission Information

	BGKLV24-25	BGKLV24-25
ENCODE_alias	brenton-graveley:EIF4G1_BGKLV24	brenton-graveley:EIF4G1-BGKLV24-K562
ENCODE_accession	ENCSR712CSN	ENCSR006GDY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-25	BGKLV24-25
Sample Name	EIF4G1_BGKLV24_25_17615	EIF4G1_BGKLV24_25_17615
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2984	6694

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
EIF4G1_BGKLV24_25_17615_AGTCAA_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1088	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17200
EIF4G1_BGKLV24_25_17615_AGTCAA_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1088	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17236
EIF4G1_BGKLV24_25_17615_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1088					GRCh38	V40	EIF4G1_BGKLV24_25_17615_AGTCAA_L007_R1_001.fastq.gz,EIF4G1_BGKLV24_25_17615_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	17272
EIF4G1_BGKLV24_25_17615_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1088					GRCh38	V40	EIF4G1_BGKLV24_25_17615/Aligned.sortedByCoord.out.bam		ENCORE2	17308
EIF4G1_BGKLV24_25_17615_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1088					GRCh38	V40	EIF4G1_BGKLV24_25_17615/Aligned.sortedByCoord.out.bam		ENCORE2	17344
EIF4G1_BGKLV24_25_17615_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1088					GRCh38	V40	EIF4G1_BGKLV24_25_17615/Aligned.sortedByCoord.out.bam		ENCORE2	17380
EIF4G1_BGKLV24_25_17615_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1088					GRCh38	V40	EIF4G1_BGKLV24_25_17615/Aligned.sortedByCoord.out.bam		ENCORE2	17416
EIF4G1_BGKLV24_25_17615_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1088					GRCh38	V40	EIF4G1_BGKLV24_25_17615_AGTCAA_L007_R1_001.fastq.gz,EIF4G1_BGKLV24_25_17615_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	17452
EIF4G1_BGKLV24_26_17616_AGTTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1089	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17201
EIF4G1_BGKLV24_26_17616_AGTTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1089	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17237
EIF4G1_BGKLV24_26_17616_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1089					GRCh38	V40	EIF4G1_BGKLV24_26_17616_AGTTCC_L007_R1_001.fastq.gz,EIF4G1_BGKLV24_26_17616_AGTTCC_L007_R2_001.fastq.gz		ENCORE2	17273
EIF4G1_BGKLV24_26_17616_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1089					GRCh38	V40	EIF4G1_BGKLV24_26_17616/Aligned.sortedByCoord.out.bam		ENCORE2	17309
EIF4G1_BGKLV24_26_17616_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1089					GRCh38	V40	EIF4G1_BGKLV24_26_17616/Aligned.sortedByCoord.out.bam		ENCORE2	17345
EIF4G1_BGKLV24_26_17616_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1089					GRCh38	V40	EIF4G1_BGKLV24_26_17616/Aligned.sortedByCoord.out.bam		ENCORE2	17381
EIF4G1_BGKLV24_26_17616_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1089					GRCh38	V40	EIF4G1_BGKLV24_26_17616/Aligned.sortedByCoord.out.bam		ENCORE2	17417
EIF4G1_BGKLV24_26_17616_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1089					GRCh38	V40	EIF4G1_BGKLV24_26_17616_AGTTCC_L007_R1_001.fastq.gz,EIF4G1_BGKLV24_26_17616_AGTTCC_L007_R2_001.fastq.gz		ENCORE2	17453