FASTKD1 RNA-Seq in HepG2

General Information


RBP	FASTKD1
Cell_Line	HepG2
Method	shRNA
Exp_Name	FASTKD1-BGHLV22-HepG2
ENCODE_series_ID	ENCSR506CST
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR728BOL
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	FASTKD1-BGHLV22-15_17752
Rep2	FASTKD1-BGHLV22-16_17753
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	71.2
Rep2_qPCR	69.1
Rep1_WB	0
Rep2_WB	0.0
Antibody Cat#	GTX107835
Antibody Lot#	LOT# 40009
Antibody DCC ID	ENCAB421NRI
Status	Released
Project	ENCODE3
ID	534

Experiment Information (Status: Released)

	BGHLV22-15	BGHLV22-16
idx	443	444
TRCN#_or_BGC#	TRCN0000129813	TRCN0000129813
shRNA_or_gRNA_sequence	CCGCTTCTGTCAACAATATAA	CCGCTTCTGTCAACAATATAA
PAM
Name	FASTKD1	FASTKD1
Sample_ID	BGHLV22-15	BGHLV22-16
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	FASTKD1	FASTKD1
qPCR_result	71.2	69.1
Ave_qPCR	70.1
RT-qPCR_primer-F	CGACATTTGGAAATTCTGGG
RT-qPCR_primer-R	TAGTCCATCCGAGCATCCTT
protein_conc	6619	6172
WB_result	0	0.0
Ave_WB	0.0
WB_DONE_date	6/4/2015	2/22/2016
MW	97kDa	WES
IP	1	1
antibody_Cat#	GTX107835	GTX107835
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	2.9	0
Rep2_TPM	2.8	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2512	2513

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-15	BGHLV22-16
Sample_ID	BGHLV22-15	BGHLV22-16
Sample Name	FASTKD1-BGHLV22-15_17752	FASTKD1-BGHLV22-16_17753
Sample Name	FASTKD1-BGHLV22-15_17752	FASTKD1-BGHLV22-16_17753
RBP	FASTKD1	FASTKD1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	782	783

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-15	BGHLV22-16
Sample #
Sample Name	FASTKD1-BGHLV22-15	FASTKD1-BGHLV22-16
Sample_Name_Alias	FASTKD1-BGHLV22-15_17752	FASTKD1-BGHLV22-16_17753
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set3/B1.png	DNA_Library_LV20-22-23/set1/H6.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/D4.png	RNA_Library_LV19-21-24/set2/E4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-15	BGHLV22-16
RBP	FASTKD1	FASTKD1
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2468	2469

Sequencing Information

	BGHLV22-15	BGHLV22-16
Sample_ID	BGHLV22-15	BGHLV22-16
Sample Name	FASTKD1-BGHLV22-15_17752	FASTKD1-BGHLV22-16_17753
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	47,610,000	52,150,000
total_aligned_reads	43,623,500	48,045,088
unique_aligned_reads	41,222,846	45,288,676
percent_uniqueAligned	0.86584	0.86843
correlation_replicates	0.991999	0.991999
spikein_reads	264,518	293,846
percent_spikeins	0.00556	0.00563
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1202	1203

Data Submission Information

	BGHLV22-15	BGHLV22-15
ENCODE_alias	brenton-graveley:FASTKD1-BGHLV22	brenton-graveley:FASTKD1-BGHLV22-HepG2
ENCODE_accession	ENCSR728BOL	ENCSR506CST
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-15	BGHLV22-15
Sample Name	FASTKD1-BGHLV22-15_17752	FASTKD1-BGHLV22-15_17752
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2923	6708

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
FASTKD1-BGHLV22-15_17752_CAGATC_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1202	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16278
FASTKD1-BGHLV22-15_17752_CAGATC_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1202	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16318
FASTKD1-BGHLV22-15_17752_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1202					GRCh38	V40	FASTKD1-BGHLV22-15_17752_CAGATC_L007_R1_001.fastq.gz,FASTKD1-BGHLV22-15_17752_CAGATC_L007_R2_001.fastq.gz		ENCORE2	16416
FASTKD1-BGHLV22-15_17752_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1202					GRCh38	V40	FASTKD1-BGHLV22-15_17752/Aligned.sortedByCoord.out.bam		ENCORE2	16456
FASTKD1-BGHLV22-15_17752_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1202					GRCh38	V40	FASTKD1-BGHLV22-15_17752/Aligned.sortedByCoord.out.bam		ENCORE2	16496
FASTKD1-BGHLV22-15_17752_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1202					GRCh38	V40	FASTKD1-BGHLV22-15_17752/Aligned.sortedByCoord.out.bam		ENCORE2	16536
FASTKD1-BGHLV22-15_17752_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1202					GRCh38	V40	FASTKD1-BGHLV22-15_17752/Aligned.sortedByCoord.out.bam		ENCORE2	16576
FASTKD1-BGHLV22-15_17752_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1202					GRCh38	V40	FASTKD1-BGHLV22-15_17752_CAGATC_L007_R1_001.fastq.gz,FASTKD1-BGHLV22-15_17752_CAGATC_L007_R2_001.fastq.gz		ENCORE2	16616
FASTKD1-BGHLV22-16_17753_ACTTGA_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1203	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16279
FASTKD1-BGHLV22-16_17753_ACTTGA_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1203	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16319
FASTKD1-BGHLV22-16_17753_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1203					GRCh38	V40	FASTKD1-BGHLV22-16_17753_ACTTGA_L007_R1_001.fastq.gz,FASTKD1-BGHLV22-16_17753_ACTTGA_L007_R2_001.fastq.gz		ENCORE2	16417
FASTKD1-BGHLV22-16_17753_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1203					GRCh38	V40	FASTKD1-BGHLV22-16_17753/Aligned.sortedByCoord.out.bam		ENCORE2	16457
FASTKD1-BGHLV22-16_17753_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1203					GRCh38	V40	FASTKD1-BGHLV22-16_17753/Aligned.sortedByCoord.out.bam		ENCORE2	16497
FASTKD1-BGHLV22-16_17753_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1203					GRCh38	V40	FASTKD1-BGHLV22-16_17753/Aligned.sortedByCoord.out.bam		ENCORE2	16537
FASTKD1-BGHLV22-16_17753_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1203					GRCh38	V40	FASTKD1-BGHLV22-16_17753/Aligned.sortedByCoord.out.bam		ENCORE2	16577
FASTKD1-BGHLV22-16_17753_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1203					GRCh38	V40	FASTKD1-BGHLV22-16_17753_ACTTGA_L007_R1_001.fastq.gz,FASTKD1-BGHLV22-16_17753_ACTTGA_L007_R2_001.fastq.gz		ENCORE2	16617