EIF2S2 RNA-Seq in K562

General Information


RBP	EIF2S2
Cell_Line	K562
Method	shRNA
Exp_Name	EIF2S2-BGKLV29-K562
ENCODE_series_ID	ENCSR487WDI
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR076PMZ
ENCODE_CN_Exp_ID	ENCSR118EFE
Rep1	EIF2S2_BGKLV29-27B
Rep2	EIF2S2_BGKLV29-28B
CN1	NTB_BGKLV29-1
CN2	NTB_BGKLV29-2
Rep1_qPCR	77.2
Rep2_qPCR	83.2
Rep1_WB	80.6
Rep2_WB	81.0
Antibody Cat#	GTX106484
Antibody Lot#	GTX106484
Antibody DCC ID	ENCAB485WQI
Status	Released
Project	ENCODE3
ID	673

Experiment Information (Status: Released)

	BGKLV29-27	BGKLV29-28
idx	560	561
TRCN#_or_BGC#	TRCN0000074788	TRCN0000074788
shRNA_or_gRNA_sequence	GAGTGGATATACCGTTGTATT	GAGTGGATATACCGTTGTATT
PAM
Name	EIF2S2/EIF2B	EIF2S2/EIF2B
Sample_ID	BGKLV29-27	BGKLV29-28
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	EIF2S2	EIF2S2
qPCR_result	77.2	83.2
Ave_qPCR	80.2
RT-qPCR_primer-F	tcaaaggaagattccaacagaaa
RT-qPCR_primer-R	gatcggcatgtgtgacaagt
protein_conc	1862	1945
WB_result	80.6	81.0
Ave_WB	80.8
WB_DONE_date	9/4/2015
MW	38kDa
IP	1	1
antibody_Cat#	GTX106484	GTX106484
Antibody DCC ID	ENCAB485WQI	ENCAB485WQI
submitted_to_DCC_date	12/7/2015
Rep1_TPM	85.0310913	0
Rep2_TPM	113.8795	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	639	640

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2S2	Product_ID: GTX106484 Lot_ID: 40135 Source: GeneTex Target Name: EIF2S2-human

Experiment Status

	BGKLV29-27	BGKLV29-28
Sample_ID	BGKLV29-27	BGKLV29-28
Sample Name	EIF2S2_BGKLV29-27B	EIF2S2_BGKLV29-28B
Sample Name	EIF2S2_BGKLV29-27B	EIF2S2_BGKLV29-28B
RBP	EIF2S2	EIF2S2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1016	1017

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-27	BGKLV29-28
Sample #
Sample Name	EIF2S2-BGKLV29-27B	EIF2S2-BGKLV29-28B
Sample_Name_Alias	EIF2S2_BGKLV29-27B	EIF2S2_BGKLV29-28B
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-03	2015-11-03
Lib_ID	Lib-151103	Lib-151103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set2/H1.png	DNA_Library_LV28-29-30/set1/H5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C1.png	RNA_Library_LV29-30-31-32/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-27	BGKLV29-28
RBP	EIF2S2	EIF2S2
Batch_ID	BGKLV29	BGKLV29
WB_result	80.600	81.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2726	2727

Sequencing Information

	BGKLV29-27	BGKLV29-28
Sample_ID	BGKLV29-27	BGKLV29-28
Sample Name	EIF2S2_BGKLV29-27B	EIF2S2_BGKLV29-28B
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	64,712,692	66,691,874
total_aligned_reads	58,126,192	59,897,940
unique_aligned_reads	53,530,012	55,066,730
percent_uniqueAligned	0.82719	0.82569
correlation_replicates	0.998216	0.998216
spikein_reads	315,614	270,844
percent_spikeins	0.00488	0.00406
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1389	1390

Data Submission Information

	BGKLV29-27	BGKLV29-27
ENCODE_alias	brenton-graveley:EIF2S2_BGKLV29-B	brenton-graveley:EIF2S2-BGKLV29-K562
ENCODE_accession	ENCSR076PMZ	ENCSR487WDI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-27	BGKLV29-27
Sample Name	EIF2S2_BGKLV29-27B	EIF2S2_BGKLV29-27B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3057	6681

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
EIF2S2_BGKLV29-27B_TTAGGC_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1389	HiSeq2500	100	paired-ended	1				NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE3	20418
EIF2S2_BGKLV29-27B_TTAGGC_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1389	HiSeq2500	100	paired-ended	2				NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE3	20448
EIF2S2_BGKLV29-27B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1389					GRCh38	V40	EIF2S2_BGKLV29-27B_TTAGGC_L007_001.R1.fastq.gz,EIF2S2_BGKLV29-27B_TTAGGC_L007_001.R2.fastq.gz		ENCORE2	20478
EIF2S2_BGKLV29-27B_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1389					GRCh38	V40	EIF2S2_BGKLV29-27B/Aligned.sortedByCoord.out.bam		ENCORE2	20508
EIF2S2_BGKLV29-27B_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1389					GRCh38	V40	EIF2S2_BGKLV29-27B/Aligned.sortedByCoord.out.bam		ENCORE2	20538
EIF2S2_BGKLV29-27B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1389					GRCh38	V40	EIF2S2_BGKLV29-27B/Aligned.sortedByCoord.out.bam		ENCORE2	20568
EIF2S2_BGKLV29-27B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1389					GRCh38	V40	EIF2S2_BGKLV29-27B/Aligned.sortedByCoord.out.bam		ENCORE2	20598
EIF2S2_BGKLV29-27B_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1389					GRCh38	V40	EIF2S2_BGKLV29-27B_TTAGGC_L007_001.R1.fastq.gz,EIF2S2_BGKLV29-27B_TTAGGC_L007_001.R2.fastq.gz		ENCORE2	20628
EIF2S2_BGKLV29-28B_TGACCA_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1390	HiSeq2500	100	paired-ended	1				NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE3	20419
EIF2S2_BGKLV29-28B_TGACCA_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1390	HiSeq2500	100	paired-ended	2				NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE3	20449
EIF2S2_BGKLV29-28B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1390					GRCh38	V40	EIF2S2_BGKLV29-28B_TGACCA_L007_001.R1.fastq.gz,EIF2S2_BGKLV29-28B_TGACCA_L007_001.R2.fastq.gz		ENCORE2	20479
EIF2S2_BGKLV29-28B_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1390					GRCh38	V40	EIF2S2_BGKLV29-28B/Aligned.sortedByCoord.out.bam		ENCORE2	20509
EIF2S2_BGKLV29-28B_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1390					GRCh38	V40	EIF2S2_BGKLV29-28B/Aligned.sortedByCoord.out.bam		ENCORE2	20539
EIF2S2_BGKLV29-28B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1390					GRCh38	V40	EIF2S2_BGKLV29-28B/Aligned.sortedByCoord.out.bam		ENCORE2	20569
EIF2S2_BGKLV29-28B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1390					GRCh38	V40	EIF2S2_BGKLV29-28B/Aligned.sortedByCoord.out.bam		ENCORE2	20599
EIF2S2_BGKLV29-28B_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1390					GRCh38	V40	EIF2S2_BGKLV29-28B_TGACCA_L007_001.R1.fastq.gz,EIF2S2_BGKLV29-28B_TGACCA_L007_001.R2.fastq.gz		ENCORE2	20629