AGO1 RNA-Seq in K562

General Information


RBP	AGO1
Cell_Line	K562
Method	shRNA
Exp_Name	AGO1-BGKLV13-K562
ENCODE_series_ID	ENCSR821NVF
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR268JDD
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	EIF2C1_BGKLV13_69
Rep2	EIF2C1_BGKLV13_70
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	58.5
Rep2_qPCR	67.2
Rep1_WB	64.6
Rep2_WB	81.1
Antibody Cat#	RN028PW
Antibody Lot#	RN028PW
Antibody DCC ID	ENCAB179WCQ
Status	Released
Project	ENCODE3
ID	382

Experiment Information (Status: Released)

	BGKLV13-69	BGKLV13-70
idx	204	205
TRCN#_or_BGC#	TRCN0000007860	TRCN0000007860
shRNA_or_gRNA_sequence	GCTGACAAGAATGAGCGAATT	GCTGACAAGAATGAGCGAATT
PAM
Name	EIF2C1	EIF2C1
Sample_ID	BGKLV13-69	BGKLV13-70
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	AGO1	AGO1
qPCR_result	58.5	67.2
Ave_qPCR	62.9
RT-qPCR_primer-F	CGCATCATCTTCTACCGAGA
RT-qPCR_primer-R	TTTCCAGTTTGATGCAGGC
protein_conc	2055	1995
WB_result	64.6	81.1
Ave_WB	72.8
WB_DONE_date	2/26/2016
MW	97KD	WES
IP	1	1
antibody_Cat#	RN028PW	RN028PW
Antibody DCC ID	ENCAB179WCQ	ENCAB179WCQ
submitted_to_DCC_date	3/8/2016
Rep1_TPM	4.95075868	0
Rep2_TPM	3.61150682	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	223	224

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AGO1	Product_ID: RN028PW Lot_ID: 2 Source: MBLI Target Name: AGO1-human

Experiment Status

	BGKLV13-69	BGKLV13-70
Sample_ID	BGKLV13-69	BGKLV13-70
Sample Name	EIF2C1_BGKLV13_69	EIF2C1_BGKLV13_70
Sample Name	EIF2C1_BGKLV13_69	EIF2C1_BGKLV13_70
RBP	AGO1	AGO1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	444	445

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-69	BGKLV13-70
Sample #
Sample Name	AGO1-BGKLV13-69	AGO1-BGKLV13-70
Sample_Name_Alias	EIF2C1_BGKLV13_69	EIF2C1_BGKLV13_70
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set2/G1.png	DNA_Library_LV13-14/set1/C7.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E3.png	RNA_Library_LV13-14-16/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-69	BGKLV13-70
RBP	AGO1	AGO1
Batch_ID	BGKLV13	BGKLV13
WB_result	64.600	81.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2168	2169

Sequencing Information

	BGKLV13-69	BGKLV13-70
Sample_ID	BGKLV13-69	BGKLV13-70
Sample Name	EIF2C1_BGKLV13_69	EIF2C1_BGKLV13_70
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	43,340,000	40,580,000
total_aligned_reads	41,436,940	38,880,276
unique_aligned_reads	38,220,870	35,706,332
percent_uniqueAligned	0.88188	0.87990
correlation_replicates	0.994395	0.994395
spikein_reads	268,136	163,838
percent_spikeins	0.00619	0.00404
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	810	811

Data Submission Information

	BGKLV13-69	BGKLV13-69
ENCODE_alias	brenton-graveley:EIF2C1_BGKLV13	brenton-graveley:AGO1-BGKLV13-K562
ENCODE_accession	ENCSR268JDD	ENCSR821NVF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-69	BGKLV13-69
Sample Name	EIF2C1_BGKLV13_69	EIF2C1_BGKLV13_69
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2771	6584

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
EIF2C1_BGKLV13_69_ATCACG_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	810	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13372
EIF2C1_BGKLV13_69_ATCACG_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	810	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13424
EIF2C1_BGKLV13_69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	810					GRCh38	V40	EIF2C1_BGKLV13_69_ATCACG_L007_R1_001.fastq.gz,EIF2C1_BGKLV13_69_ATCACG_L007_R2_001.fastq.gz		ENCORE2	13476
EIF2C1_BGKLV13_69_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	810					GRCh38	V40	EIF2C1_BGKLV13_69/Aligned.sortedByCoord.out.bam		ENCORE2	13528
EIF2C1_BGKLV13_69_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	810					GRCh38	V40	EIF2C1_BGKLV13_69/Aligned.sortedByCoord.out.bam		ENCORE2	13580
EIF2C1_BGKLV13_69_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	810					GRCh38	V40	EIF2C1_BGKLV13_69/Aligned.sortedByCoord.out.bam		ENCORE2	13632
EIF2C1_BGKLV13_69_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	810					GRCh38	V40	EIF2C1_BGKLV13_69/Aligned.sortedByCoord.out.bam		ENCORE2	13684
EIF2C1_BGKLV13_69_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	810					GRCh38	V40	EIF2C1_BGKLV13_69_ATCACG_L007_R1_001.fastq.gz,EIF2C1_BGKLV13_69_ATCACG_L007_R2_001.fastq.gz		ENCORE2	13736
EIF2C1_BGKLV13_70_CGATGT_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	811	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13373
EIF2C1_BGKLV13_70_CGATGT_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	811	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13425
EIF2C1_BGKLV13_70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	811					GRCh38	V40	EIF2C1_BGKLV13_70_CGATGT_L007_R1_001.fastq.gz,EIF2C1_BGKLV13_70_CGATGT_L007_R2_001.fastq.gz		ENCORE2	13477
EIF2C1_BGKLV13_70_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	811					GRCh38	V40	EIF2C1_BGKLV13_70/Aligned.sortedByCoord.out.bam		ENCORE2	13529
EIF2C1_BGKLV13_70_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	811					GRCh38	V40	EIF2C1_BGKLV13_70/Aligned.sortedByCoord.out.bam		ENCORE2	13581
EIF2C1_BGKLV13_70_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	811					GRCh38	V40	EIF2C1_BGKLV13_70/Aligned.sortedByCoord.out.bam		ENCORE2	13633
EIF2C1_BGKLV13_70_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	811					GRCh38	V40	EIF2C1_BGKLV13_70/Aligned.sortedByCoord.out.bam		ENCORE2	13685
EIF2C1_BGKLV13_70_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	811					GRCh38	V40	EIF2C1_BGKLV13_70_CGATGT_L007_R1_001.fastq.gz,EIF2C1_BGKLV13_70_CGATGT_L007_R2_001.fastq.gz		ENCORE2	13737