TIA1 RNA-Seq in K562

General Information


RBP	TIA1
Cell_Line	K562
Method	shRNA
Exp_Name	TIA1-BGKLV11-K562
ENCODE_series_ID	ENCSR425NUL
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR694LKY
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	TIA1-LV11-59
Rep2	TIA1-LV11-60
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	62.2
Rep2_qPCR	53.1
Rep1_WB	91.3
Rep2_WB	91.5
Antibody Cat#	RN014P
Antibody Lot#	RN014P
Antibody DCC ID	ENCAB000BGC
Status	Released
Project	ENCODE3
ID	327

Experiment Information (Status: Released)

	BGKLV11-59	BGKLV11-60
idx	128	129
TRCN#_or_BGC#	TRCN0000074463	TRCN0000074463
shRNA_or_gRNA_sequence	GCCGTTGTTTACTTAAAGATT	GCCGTTGTTTACTTAAAGATT
PAM
Name	TIA1	TIA1
Sample_ID	BGKLV11-59	BGKLV11-60
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	TIA1	TIA1
qPCR_result	62.2	53.1
Ave_qPCR	57.6
RT-qPCR_primer-F	CATATGGAATGTATGGCCAGG
RT-qPCR_primer-R	GCGGTTGCACTCCATAATTT
protein_conc	2048	2183
WB_result	91.3	91.5
Ave_WB	91.4
WB_DONE_date
MW	43kDa
IP	1	1
antibody_Cat#	RN014P	RN014P
Antibody DCC ID	ENCAB000BGC	ENCAB000BGC
submitted_to_DCC_date	4/2/2015
Rep1_TPM	10.1024171	0
Rep2_TPM	8.78850489	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note		9
ID	143	144

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TIA1	Product_ID: RN014P Lot_ID: 1 Source: MBLI Target Name: TIA1-human

Experiment Status

	BGKLV11-59	BGKLV11-60
Sample_ID	BGKLV11-59	BGKLV11-60
Sample Name	TIA1-LV11-59	TIA1-LV11-60
Sample Name	TIA1-LV11-59	TIA1-LV11-60
RBP	TIA1	TIA1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	368	369

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-59	BGKLV11-60
Sample #
Sample Name	TIA1-BGKLV11-59	TIA1-BGKLV11-60
Sample_Name_Alias	TIA1-LV11-59	TIA1-LV11-60
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set3/H2.png	DNA_Library_LV11/set4/B1.png
RIN	9.0	8.9
libSample_RNA_Well	RNA_Library_LV11/set1/E6.png	RNA_Library_LV11/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-59	BGKLV11-60
RBP	TIA1	TIA1
Batch_ID	BGKLV11	BGKLV11
WB_result	91.300	91.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1990	1991

Sequencing Information

	BGKLV11-59	BGKLV11-60
Sample_ID	BGKLV11-59	BGKLV11-60
Sample Name	TIA1-LV11-59	TIA1-LV11-60
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	58,250,000	53,230,000
total_aligned_reads	48,073,492	42,022,926
unique_aligned_reads	44,053,370	38,427,876
percent_uniqueAligned	0.75628	0.72192
correlation_replicates	0.995369	0.995369
spikein_reads	321,452	207,570
percent_spikeins	0.00552	0.00390
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	690	691

Data Submission Information

	BGKLV11-59	BGKLV11-59
ENCODE_alias	brenton-graveley:TIA1-LV11	brenton-graveley:TIA1-BGKLV11-K562
ENCODE_accession	ENCSR694LKY	ENCSR425NUL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-59	BGKLV11-59
Sample Name	TIA1-LV11-59	TIA1-LV11-59
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2733	7008

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
TIA1-LV11-59_CGTACG_L008_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	690	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12411
TIA1-LV11-59_CGTACG_L008_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	690	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12459
TIA1-LV11-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	690					GRCh38	V40	TIA1-LV11-59_CGTACG_L008_R1_001.fastq.gz,TIA1-LV11-59_CGTACG_L008_R2_001.fastq.gz		ENCORE2	12507
TIA1-LV11-59_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	690					GRCh38	V40	TIA1-LV11-59/Aligned.sortedByCoord.out.bam		ENCORE2	12555
TIA1-LV11-59_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	690					GRCh38	V40	TIA1-LV11-59/Aligned.sortedByCoord.out.bam		ENCORE2	12603
TIA1-LV11-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	690					GRCh38	V40	TIA1-LV11-59/Aligned.sortedByCoord.out.bam		ENCORE2	12651
TIA1-LV11-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	690					GRCh38	V40	TIA1-LV11-59/Aligned.sortedByCoord.out.bam		ENCORE2	12699
TIA1-LV11-59_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	690					GRCh38	V40	TIA1-LV11-59_CGTACG_L008_R1_001.fastq.gz,TIA1-LV11-59_CGTACG_L008_R2_001.fastq.gz		ENCORE2	12747
TIA1-LV11-60_GAGTGG_L008_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	691	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12412
TIA1-LV11-60_GAGTGG_L008_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	691	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12460
TIA1-LV11-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	691					GRCh38	V40	TIA1-LV11-60_GAGTGG_L008_R1_001.fastq.gz,TIA1-LV11-60_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	12508
TIA1-LV11-60_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	691					GRCh38	V40	TIA1-LV11-60/Aligned.sortedByCoord.out.bam		ENCORE2	12556
TIA1-LV11-60_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	691					GRCh38	V40	TIA1-LV11-60/Aligned.sortedByCoord.out.bam		ENCORE2	12604
TIA1-LV11-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	691					GRCh38	V40	TIA1-LV11-60/Aligned.sortedByCoord.out.bam		ENCORE2	12652
TIA1-LV11-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	691					GRCh38	V40	TIA1-LV11-60/Aligned.sortedByCoord.out.bam		ENCORE2	12700
TIA1-LV11-60_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	691					GRCh38	V40	TIA1-LV11-60_GAGTGG_L008_R1_001.fastq.gz,TIA1-LV11-60_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	12748