TIAL1 RNA-Seq in K562

General Information


RBP	TIAL1
Cell_Line	K562
Method	shRNA
Exp_Name	TIAL1-BGKLV21-K562
ENCODE_series_ID	ENCSR101JTW
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR927TSP
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	TIAL1_BGKLV21_61_17588
Rep2	TIAL1_BGKLV21_62_17589
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	47.2
Rep2_qPCR	44.2
Rep1_WB	59.4
Rep2_WB	63.2
Antibody Cat#	RN059PW
Antibody Lot#	RN059PW
Antibody DCC ID	ENCAB050ZSG
Status	Released
Project	ENCODE3
ID	520

Experiment Information (Status: Released)

	BGKLV21-61	BGKLV21-61	BGKLV21-61	BGKLV21-62	BGKLV21-62	BGKLV21-62
idx	332	332	332	333	333	333
TRCN#_or_BGC#	TRCN0000017211	TRCN0000017211	TRCN0000017211	TRCN0000017211	TRCN0000017211	TRCN0000017211
shRNA_or_gRNA_sequence	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA
PAM
Name	TIAL1	TIAL1	TIAL1	TIAL1	TIAL1	TIAL1
Sample_ID	BGKLV21-61	BGKLV21-61	BGKLV21-61	BGKLV21-62	BGKLV21-62	BGKLV21-62
transduction_Date	10/9/2014	10/9/2014	10/9/2014	10/9/2014	10/9/2014	10/9/2014
days
RBP_name	TIAL1	TIAL1	TIAL1	TIAL1	TIAL1	TIAL1
qPCR_result	47.2	47.2	47.2	44.2	44.2	44.2
Ave_qPCR	45.7	45.7	45.7
RT-qPCR_primer-F	ctcgtaaaccacctgcacct	ctcgtaaaccacctgcacct	ctcgtaaaccacctgcacct
RT-qPCR_primer-R	ttcctccacagtacacagtacaa	ttcctccacagtacacagtacaa	ttcctccacagtacacagtacaa
protein_conc	2954	2954	2954	3378	3378	3378
WB_result	59.4	81.3	82.6	63.2	79.2	80.9
Ave_WB	61.3	80.2	81.7
WB_DONE_date	3/6/2015	6/26/2023	6/26/2023
MW	41kDa	41kDa	41kDa
IP	1			1
antibody_Cat#	RN059PW	8509S	8611S	RN059PW	LOT # 2	LOT# 1
Antibody DCC ID	ENCAB050ZSG			ENCAB050ZSG
submitted_to_DCC_date	8/6/2015	1/8/2024	1/8/2024
Rep1_TPM	29.4790811	0	0	0	0	0
Rep2_TPM	23.6724867	0	0	0	0	0
Action
Library_start_date	5/19/2015			5/19/2015
repeat_library
Note
ID	369	371	373	370	372	374

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TIAL1	Product_ID: RN059PW Lot_ID: 1 Source: MBLI Target Name: TIAL1-human
TIAL1	Product_ID: 8509S Lot_ID: 2 Source: Cell Signaling Technology Target Name: TIAL1-human
TIAL1	Product_ID: 8611S Lot_ID: 1 Source: Cell Signaling Technology Target Name: TIAL1-human

Experiment Status

	BGKLV21-61	BGKLV21-62
Sample_ID	BGKLV21-61	BGKLV21-62
Sample Name	TIAL1_BGKLV21_61_17588	TIAL1_BGKLV21_62_17589
Sample Name	TIAL1_BGKLV21_61_17588	TIAL1_BGKLV21_62_17589
RBP	TIAL1	TIAL1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	774	775

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-61	BGKLV21-62
Sample #
Sample Name	TIAL1-BGKLV21-61	TIAL1-BGKLV21-62
Sample_Name_Alias	TIAL1_BGKLV21_61_17588	TIAL1_BGKLV21_62_17589
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/G8.png	DNA_Library_LV21-24/set1/H8.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G11.png	RNA_Library_LV19-21-24/set1/H11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-61	BGKLV21-62
RBP	TIAL1	TIAL1
Batch_ID	BGKLV21	BGKLV21
WB_result	59.400	63.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2460	2461

Sequencing Information

	BGKLV21-61	BGKLV21-62
Sample_ID	BGKLV21-61	BGKLV21-62
Sample Name	TIAL1_BGKLV21_61_17588	TIAL1_BGKLV21_62_17589
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	36,490,000	36,570,000
total_aligned_reads	33,152,474	33,777,494
unique_aligned_reads	30,506,490	31,100,962
percent_uniqueAligned	0.83602	0.85045
correlation_replicates	0.998562	0.998562
spikein_reads	157,492	156,910
percent_spikeins	0.00432	0.00429
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1066	1067

Data Submission Information

	BGKLV21-61	BGKLV21-61
ENCODE_alias	brenton-graveley:TIAL1_BGKLV21	brenton-graveley:TIAL1-BGKLV21-K562
ENCODE_accession	ENCSR927TSP	ENCSR101JTW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-61	BGKLV21-61
Sample Name	TIAL1_BGKLV21_61_17588	TIAL1_BGKLV21_61_17588
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2973	7010

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
TIAL1_BGKLV21_61_17588_CAGATC_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1066	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15958
TIAL1_BGKLV21_61_17588_CAGATC_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1066	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	16002
TIAL1_BGKLV21_61_17588_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1066					GRCh38	V40	TIAL1_BGKLV21_61_17588_CAGATC_L004_R1_001.fastq.gz,TIAL1_BGKLV21_61_17588_CAGATC_L004_R2_001.fastq.gz		ENCORE2	16046
TIAL1_BGKLV21_61_17588_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1066					GRCh38	V40	TIAL1_BGKLV21_61_17588/Aligned.sortedByCoord.out.bam		ENCORE2	16090
TIAL1_BGKLV21_61_17588_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1066					GRCh38	V40	TIAL1_BGKLV21_61_17588/Aligned.sortedByCoord.out.bam		ENCORE2	16134
TIAL1_BGKLV21_61_17588_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1066					GRCh38	V40	TIAL1_BGKLV21_61_17588/Aligned.sortedByCoord.out.bam		ENCORE2	16178
TIAL1_BGKLV21_61_17588_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1066					GRCh38	V40	TIAL1_BGKLV21_61_17588/Aligned.sortedByCoord.out.bam		ENCORE2	16222
TIAL1_BGKLV21_61_17588_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1066					GRCh38	V40	TIAL1_BGKLV21_61_17588_CAGATC_L004_R1_001.fastq.gz,TIAL1_BGKLV21_61_17588_CAGATC_L004_R2_001.fastq.gz		ENCORE2	16266
TIAL1_BGKLV21_62_17589_ACTTGA_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1067	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15959
TIAL1_BGKLV21_62_17589_ACTTGA_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1067	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	16003
TIAL1_BGKLV21_62_17589_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1067					GRCh38	V40	TIAL1_BGKLV21_62_17589_ACTTGA_L004_R1_001.fastq.gz,TIAL1_BGKLV21_62_17589_ACTTGA_L004_R2_001.fastq.gz		ENCORE2	16047
TIAL1_BGKLV21_62_17589_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1067					GRCh38	V40	TIAL1_BGKLV21_62_17589/Aligned.sortedByCoord.out.bam		ENCORE2	16091
TIAL1_BGKLV21_62_17589_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1067					GRCh38	V40	TIAL1_BGKLV21_62_17589/Aligned.sortedByCoord.out.bam		ENCORE2	16135
TIAL1_BGKLV21_62_17589_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1067					GRCh38	V40	TIAL1_BGKLV21_62_17589/Aligned.sortedByCoord.out.bam		ENCORE2	16179
TIAL1_BGKLV21_62_17589_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1067					GRCh38	V40	TIAL1_BGKLV21_62_17589/Aligned.sortedByCoord.out.bam		ENCORE2	16223
TIAL1_BGKLV21_62_17589_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1067					GRCh38	V40	TIAL1_BGKLV21_62_17589_ACTTGA_L004_R1_001.fastq.gz,TIAL1_BGKLV21_62_17589_ACTTGA_L004_R2_001.fastq.gz		ENCORE2	16267