TIA1 RNA-Seq in HepG2

General Information


RBP	TIA1
Cell_Line	HepG2
Method	shRNA
Exp_Name	TIA1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR817LLK
Batch_ID	BGHLV12
Pool ID	Pool-140801
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR057GCF
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	TIA1-BGHLV12-87
Rep2	TIA1-BGHLV12-88
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	72.8
Rep2_qPCR	71.6
Rep1_WB	94.3
Rep2_WB	98.0
Antibody Cat#	RN014P
Antibody Lot#	RN014P
Antibody DCC ID	ENCAB000BGC
Status	Released
Project	ENCODE3
ID	359

Experiment Information (Status: Released)

	BGHLV12-87	BGHLV12-88
idx	89	90
TRCN#_or_BGC#	TRCN0000074463	TRCN0000074463
shRNA_or_gRNA_sequence	GCCGTTGTTTACTTAAAGATT	GCCGTTGTTTACTTAAAGATT
PAM
Name	TIA1	TIA1
Sample_ID	BGHLV12-87	BGHLV12-88
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	TIA1	TIA1
qPCR_result	72.8	71.6
Ave_qPCR	72.2
RT-qPCR_primer-F	CATATGGAATGTATGGCCAGG
RT-qPCR_primer-R	GCGGTTGCACTCCATAATTT
protein_conc	3860	4607
WB_result	94.3	98.0
Ave_WB	96.2
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	18.7	0
Rep2_TPM	17.1	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2146	2147

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

	BGHLV12-87	BGHLV12-88
Sample_ID	BGHLV12-87	BGHLV12-88
Sample Name	TIA1-BGHLV12-87	TIA1-BGHLV12-88
Sample Name	TIA1-BGHLV12-87	TIA1-BGHLV12-88
RBP	TIA1	TIA1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	436	437

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-87	BGHLV12-88
Sample #
Sample Name	TIA1-BGHLV12-87	TIA1-BGHLV12-88
Sample_Name_Alias	TIA1-BGHLV12-87	TIA1-BGHLV12-88
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/A5.png	DNA_Library_LV12/set3/B5.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV12/set1/A9.png	RNA_Library_LV12/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-87	BGHLV12-88
RBP	TIA1	TIA1
Batch_ID	BGHLV12	BGHLV12
WB_result	94.300	98.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2060	2061

Sequencing Information

	BGHLV12-87	BGHLV12-88
Sample_ID	BGHLV12-87	BGHLV12-88
Sample Name	TIA1-BGHLV12-87	TIA1-BGHLV12-88
Pool ID	Pool-140801	Pool-140801
LocalServer_folder	set12	set12
total_reads	61,300,000	53,570,000
total_aligned_reads	56,562,784	48,430,836
unique_aligned_reads	53,537,102	45,793,194
percent_uniqueAligned	0.87336	0.85483
correlation_replicates	0.995920	0.995920
spikein_reads	342,242	388,708
percent_spikeins	0.00558	0.00726
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	760	761

Data Submission Information

	BGHLV12-87	BGHLV12-87
ENCODE_alias	brenton-graveley:TIA1-BGHLV12	brenton-graveley:TIA1-BGHLV12-HepG2
ENCODE_accession	ENCSR057GCF	ENCSR817LLK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-87	BGHLV12-87
Sample Name	TIA1-BGHLV12-87	TIA1-BGHLV12-87
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2767	7007

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-BGHLV12-87_GTCCGC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	760	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12819
TIA1-BGHLV12-87_GTCCGC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	760	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12888
TIA1-BGHLV12-87_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	760					GRCh38	V40	TIA1-BGHLV12-87_GTCCGC_L006_R1_001.fastq.gz,TIA1-BGHLV12-87_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	12958
TIA1-BGHLV12-87_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	760					GRCh38	V40	TIA1-BGHLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	13028
TIA1-BGHLV12-87_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	760					GRCh38	V40	TIA1-BGHLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	13098
TIA1-BGHLV12-87_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	760					GRCh38	V40	TIA1-BGHLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	13168
TIA1-BGHLV12-87_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	760					GRCh38	V40	TIA1-BGHLV12-87/Aligned.sortedByCoord.out.bam		ENCORE2	13238
TIA1-BGHLV12-87_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	760					GRCh38	V40	TIA1-BGHLV12-87_GTCCGC_L006_R1_001.fastq.gz,TIA1-BGHLV12-87_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	13308
TIA1-BGHLV12-88_GTGAAA_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	761	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12820
TIA1-BGHLV12-88_GTGAAA_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	761	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12889
TIA1-BGHLV12-88_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	761					GRCh38	V40	TIA1-BGHLV12-88_GTGAAA_L006_R1_001.fastq.gz,TIA1-BGHLV12-88_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	12959
TIA1-BGHLV12-88_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	761					GRCh38	V40	TIA1-BGHLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	13029
TIA1-BGHLV12-88_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	761					GRCh38	V40	TIA1-BGHLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	13099
TIA1-BGHLV12-88_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	761					GRCh38	V40	TIA1-BGHLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	13169
TIA1-BGHLV12-88_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	761					GRCh38	V40	TIA1-BGHLV12-88/Aligned.sortedByCoord.out.bam		ENCORE2	13239
TIA1-BGHLV12-88_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	761					GRCh38	V40	TIA1-BGHLV12-88_GTGAAA_L006_R1_001.fastq.gz,TIA1-BGHLV12-88_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	13309