AATF RNA-Seq in HepG2

General Information


RBP	AATF
Cell_Line	HepG2
Method	shRNA
Exp_Name	AATF-BGHLV14-HepG2
ENCODE_series_ID	ENCSR634FMS
Batch_ID	BGHLV14
Pool ID	Pool-140901
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR424YSV
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	AATF_BGHLV14-3
Rep2	AATF_BGHLV14-4
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	76.0
Rep2_qPCR	64.5
Rep1_WB	77.5
Rep2_WB	81.1
Antibody Cat#	A301-032A
Antibody Lot#	A301-032A
Antibody DCC ID	ENCAB064GNR
Status	Released
Project	ENCODE3
ID	384

Experiment Information (Status: Released)

	BGHLV14-3	BGHLV14-4
idx	97	98
TRCN#_or_BGC#	TRCN0000017388	TRCN0000017388
shRNA_or_gRNA_sequence	CACTTCAGAAATGGCACGATA	CACTTCAGAAATGGCACGATA
PAM
Name	AATF	AATF
Sample_ID	BGHLV14-3	BGHLV14-4
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	AATF	AATF
qPCR_result	76.0	64.5
Ave_qPCR	70.3
RT-qPCR_primer-F	cagtgaggatgatggtgtgg
RT-qPCR_primer-R	tggtcccacagtgctatctg
protein_conc	4249	4332
WB_result	77.5	81.1
Ave_WB	79.3
WB_DONE_date	7/24/2014
MW	63kDa
IP	1	1
antibody_Cat#	A301-032A	A301-032A
Antibody DCC ID	ENCAB064GNR	ENCAB064GNR
submitted_to_DCC_date	4/2/2015
Rep1_TPM	34.1	0
Rep2_TPM	36.2	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2154	2155

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AATF	Product_ID: A301-032A Lot_ID: 1 Source: Bethyl Labs Target Name: AATF-human

Experiment Status

	BGHLV14-3	BGHLV14-4
Sample_ID	BGHLV14-3	BGHLV14-4
Sample Name	AATF_BGHLV14-3	AATF_BGHLV14-4
Sample Name	AATF_BGHLV14-3	AATF_BGHLV14-4
RBP	AATF	AATF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	490	491

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-3	BGHLV14-4
Sample #
Sample Name	AATF-BGHLV14-3	AATF-BGHLV14-4
Sample_Name_Alias	AATF_BGHLV14-3	AATF_BGHLV14-4
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/H7.png	DNA_Library_LV13-14/set1/A8.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C4.png	RNA_Library_LV13-14-16/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-3	BGHLV14-4
RBP	AATF	AATF
Batch_ID	BGHLV14	BGHLV14
WB_result	77.500	81.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2174	2175

Sequencing Information

	BGHLV14-3	BGHLV14-4
Sample_ID	BGHLV14-3	BGHLV14-4
Sample Name	AATF_BGHLV14-3	AATF_BGHLV14-4
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set14	set14
total_reads	42,260,000	44,890,000
total_aligned_reads	39,669,976	42,093,798
unique_aligned_reads	37,243,188	39,461,602
percent_uniqueAligned	0.88129	0.87907
correlation_replicates	0.997987	0.997987
spikein_reads	117,648	115,994
percent_spikeins	0.00278	0.00258
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	816	817

Data Submission Information

	BGHLV14-3	BGHLV14-3
ENCODE_alias	brenton-graveley:AATF_BGHLV14	brenton-graveley:AATF-BGHLV14-HepG2
ENCODE_accession	ENCSR424YSV	ENCSR634FMS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-3	BGHLV14-3
Sample Name	AATF_BGHLV14-3	AATF_BGHLV14-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2794	6574

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
AATF_BGHLV14-3_CAGATC_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	816	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13782
AATF_BGHLV14-3_CAGATC_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	816	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13844
AATF_BGHLV14-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	816					GRCh38	V40	AATF_BGHLV14-3_CAGATC_L008_R1_001.fastq.gz,AATF_BGHLV14-3_CAGATC_L008_R2_001.fastq.gz		ENCORE2	13906
AATF_BGHLV14-3_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	816					GRCh38	V40	AATF_BGHLV14-3/Aligned.sortedByCoord.out.bam		ENCORE2	13968
AATF_BGHLV14-3_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	816					GRCh38	V40	AATF_BGHLV14-3/Aligned.sortedByCoord.out.bam		ENCORE2	14030
AATF_BGHLV14-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	816					GRCh38	V40	AATF_BGHLV14-3/Aligned.sortedByCoord.out.bam		ENCORE2	14092
AATF_BGHLV14-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	816					GRCh38	V40	AATF_BGHLV14-3/Aligned.sortedByCoord.out.bam		ENCORE2	14154
AATF_BGHLV14-3_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	816					GRCh38	V40	AATF_BGHLV14-3_CAGATC_L008_R1_001.fastq.gz,AATF_BGHLV14-3_CAGATC_L008_R2_001.fastq.gz		ENCORE2	14216
AATF_BGHLV14-4_ACTTGA_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	817	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13783
AATF_BGHLV14-4_ACTTGA_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	817	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13845
AATF_BGHLV14-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	817					GRCh38	V40	AATF_BGHLV14-4_ACTTGA_L008_R1_001.fastq.gz,AATF_BGHLV14-4_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	13907
AATF_BGHLV14-4_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	817					GRCh38	V40	AATF_BGHLV14-4/Aligned.sortedByCoord.out.bam		ENCORE2	13969
AATF_BGHLV14-4_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	817					GRCh38	V40	AATF_BGHLV14-4/Aligned.sortedByCoord.out.bam		ENCORE2	14031
AATF_BGHLV14-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	817					GRCh38	V40	AATF_BGHLV14-4/Aligned.sortedByCoord.out.bam		ENCORE2	14093
AATF_BGHLV14-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	817					GRCh38	V40	AATF_BGHLV14-4/Aligned.sortedByCoord.out.bam		ENCORE2	14155
AATF_BGHLV14-4_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	817					GRCh38	V40	AATF_BGHLV14-4_ACTTGA_L008_R1_001.fastq.gz,AATF_BGHLV14-4_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	14217