TIAL1 RNA-Seq in HepG2

General Information


RBP	TIAL1
Cell_Line	HepG2
Method	shRNA
Exp_Name	TIAL1-BGHLV20-HepG2
ENCODE_series_ID	ENCSR744QNE
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR450VQO
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	TIAL1-BGHLV20-59_17738
Rep2	TIAL1-BGHLV20-60_17739
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	53.0
Rep2_qPCR	43.6
Rep1_WB	87.4
Rep2_WB	85.3
Antibody Cat#	RN059PW
Antibody Lot#	RN059PW
Antibody DCC ID	ENCAB050ZSG
Status	Released
Project	ENCODE3
ID	504

Experiment Information (Status: Released)

	BGHLV20-59	BGHLV20-60
idx	423	424
TRCN#_or_BGC#	TRCN0000017211	TRCN0000017211
shRNA_or_gRNA_sequence	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA
PAM
Name	TIAL1	TIAL1
Sample_ID	BGHLV20-59	BGHLV20-60
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	TIAL1	TIAL1
qPCR_result	53.0	43.6
Ave_qPCR	48.3
RT-qPCR_primer-F	ctcgtaaaccacctgcacct
RT-qPCR_primer-R	ttcctccacagtacacagtacaa
protein_conc	3693	3305
WB_result	87.4	85.3
Ave_WB	86.4
WB_DONE_date	7/15/2015	very light band
MW	41kDa
IP	1	1
antibody_Cat#	RN059PW	RN059PW
Antibody DCC ID	ENCAB050ZSG	ENCAB050ZSG
submitted_to_DCC_date	8/6/2015
Rep1_TPM	39.4	0
Rep2_TPM	40.1	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2490	2491

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

Experiment Status

	BGHLV20-59	BGHLV20-60
Sample_ID	BGHLV20-59	BGHLV20-60
Sample Name	TIAL1-BGHLV20-59_17738	TIAL1-BGHLV20-60_17739
Sample Name	TIAL1-BGHLV20-59_17738	TIAL1-BGHLV20-60_17739
RBP	TIAL1	TIAL1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	740	741

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-59	BGHLV20-60
Sample #
Sample Name	TIAL1-BGHLV20-59	TIAL1-BGHLV20-60
Sample_Name_Alias	TIAL1-BGHLV20-59_17738	TIAL1-BGHLV20-60_17739
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A5.png	DNA_Library_LV20-22-23/set1/B5.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/H3.png	RNA_Library_LV20-22-24/set1/D11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-59	BGHLV20-60
RBP	TIAL1	TIAL1
Batch_ID	BGHLV20	BGHLV20
WB_result	87.400	85.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2426	2427

Sequencing Information

	BGHLV20-59	BGHLV20-60
Sample_ID	BGHLV20-59	BGHLV20-60
Sample Name	TIAL1-BGHLV20-59_17738	TIAL1-BGHLV20-60_17739
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	49,270,000	39,320,000
total_aligned_reads	44,433,698	35,939,134
unique_aligned_reads	41,828,312	33,846,834
percent_uniqueAligned	0.84896	0.86080
correlation_replicates	0.987089	0.987089
spikein_reads	196,038	169,994
percent_spikeins	0.00398	0.00432
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1194	1195

Data Submission Information

	BGHLV20-59	BGHLV20-59
ENCODE_alias	brenton-graveley:TIAL1-BHLV20	brenton-graveley:TIAL1-BGHLV20-HepG2
ENCODE_accession	ENCSR450VQO	ENCSR744QNE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-59	BGHLV20-59
Sample Name	TIAL1-BGHLV20-59_17738	TIAL1-BGHLV20-59_17738
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2919	7009

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-BGHLV20-59_17738_GATCAG_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1194	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15622
TIAL1-BGHLV20-59_17738_GATCAG_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1194	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15664
TIAL1-BGHLV20-59_17738_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1194					GRCh38	V40	TIAL1-BGHLV20-59_17738_GATCAG_L005_R1_001.fastq.gz,TIAL1-BGHLV20-59_17738_GATCAG_L005_R2_001.fastq.gz		ENCORE2	15706
TIAL1-BGHLV20-59_17738_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1194					GRCh38	V40	TIAL1-BGHLV20-59_17738/Aligned.sortedByCoord.out.bam		ENCORE2	15748
TIAL1-BGHLV20-59_17738_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1194					GRCh38	V40	TIAL1-BGHLV20-59_17738/Aligned.sortedByCoord.out.bam		ENCORE2	15790
TIAL1-BGHLV20-59_17738_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1194					GRCh38	V40	TIAL1-BGHLV20-59_17738/Aligned.sortedByCoord.out.bam		ENCORE2	15832
TIAL1-BGHLV20-59_17738_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1194					GRCh38	V40	TIAL1-BGHLV20-59_17738/Aligned.sortedByCoord.out.bam		ENCORE2	15874
TIAL1-BGHLV20-59_17738_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1194					GRCh38	V40	TIAL1-BGHLV20-59_17738_GATCAG_L005_R1_001.fastq.gz,TIAL1-BGHLV20-59_17738_GATCAG_L005_R2_001.fastq.gz		ENCORE2	15916
TIAL1-BGHLV20-60_17739_TAGCTT_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1195	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15623
TIAL1-BGHLV20-60_17739_TAGCTT_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1195	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15665
TIAL1-BGHLV20-60_17739_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1195					GRCh38	V40	TIAL1-BGHLV20-60_17739_TAGCTT_L005_R1_001.fastq.gz,TIAL1-BGHLV20-60_17739_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	15707
TIAL1-BGHLV20-60_17739_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1195					GRCh38	V40	TIAL1-BGHLV20-60_17739/Aligned.sortedByCoord.out.bam		ENCORE2	15749
TIAL1-BGHLV20-60_17739_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1195					GRCh38	V40	TIAL1-BGHLV20-60_17739/Aligned.sortedByCoord.out.bam		ENCORE2	15791
TIAL1-BGHLV20-60_17739_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1195					GRCh38	V40	TIAL1-BGHLV20-60_17739/Aligned.sortedByCoord.out.bam		ENCORE2	15833
TIAL1-BGHLV20-60_17739_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1195					GRCh38	V40	TIAL1-BGHLV20-60_17739/Aligned.sortedByCoord.out.bam		ENCORE2	15875
TIAL1-BGHLV20-60_17739_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1195					GRCh38	V40	TIAL1-BGHLV20-60_17739_TAGCTT_L005_R1_001.fastq.gz,TIAL1-BGHLV20-60_17739_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	15917