AATF RNA-Seq in K562

General Information


RBP	AATF
Cell_Line	K562
Method	shRNA
Exp_Name	AATF-BGKLV13-K562
ENCODE_series_ID	ENCSR146UCW
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR973QSV
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	AATF_BGKLV13_13
Rep2	AATF_BGKLV13_14
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	69.8
Rep2_qPCR	80.3
Rep1_WB	57.5
Rep2_WB	42.0
Antibody Cat#	A301-032A
Antibody Lot#	A301-032A
Antibody DCC ID	ENCAB064GNR
Status	Released
Project	ENCODE3
ID	364

Experiment Information (Status: Released)

	BGKLV13-13	BGKLV13-14
idx	146	147
TRCN#_or_BGC#	TRCN0000017388	TRCN0000017388
shRNA_or_gRNA_sequence	CACTTCAGAAATGGCACGATA	CACTTCAGAAATGGCACGATA
PAM
Name	AATF	AATF
Sample_ID	BGKLV13-13	BGKLV13-14
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	AATF	AATF
qPCR_result	69.8	80.3
Ave_qPCR	75.0
RT-qPCR_primer-F	cagtgaggatgatggtgtgg
RT-qPCR_primer-R	tggtcccacagtgctatctg
protein_conc	1918	1974
WB_result	57.5	42.0
Ave_WB	49.8
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	111.498807	0
Rep2_TPM	98.5683717	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note		3
ID	161	162

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

	BGKLV13-13	BGKLV13-14
Sample_ID	BGKLV13-13	BGKLV13-14
Sample Name	AATF_BGKLV13_13	AATF_BGKLV13_14
Sample Name	AATF_BGKLV13_13	AATF_BGKLV13_14
RBP	AATF	AATF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	438	439

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-13	BGKLV13-14
Sample #
Sample Name	AATF-BGKLV13-13	AATF-BGKLV13-14
Sample_Name_Alias	AATF_BGKLV13_13	AATF_BGKLV13_14
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D2.png	DNA_Library_LV13-14/set1/E2.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/G10.png	RNA_Library_LV12/set1/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-13	BGKLV13-14
RBP	AATF	AATF
Batch_ID	BGKLV13	BGKLV13
WB_result	57.500	42.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2130	2131

Sequencing Information

	BGKLV13-13	BGKLV13-14
Sample_ID	BGKLV13-13	BGKLV13-14
Sample Name	AATF_BGKLV13_13	AATF_BGKLV13_14
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	49,580,000	48,240,000
total_aligned_reads	46,091,682	44,902,016
unique_aligned_reads	42,488,504	41,449,538
percent_uniqueAligned	0.85697	0.85924
correlation_replicates	0.993986	0.993986
spikein_reads	100,648	139,610
percent_spikeins	0.00203	0.00289
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	772	773

Data Submission Information

	BGKLV13-13	BGKLV13-13
ENCODE_alias	brenton-graveley:AATF_BGKLV13	brenton-graveley:AATF-BGKLV13-K562
ENCODE_accession	ENCSR973QSV	ENCSR146UCW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-13	BGKLV13-13
Sample Name	AATF_BGKLV13_13	AATF_BGKLV13_13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2768	6575

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_BGKLV13_13_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	772	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13366
AATF_BGKLV13_13_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	772	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13418
AATF_BGKLV13_13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	772					GRCh38	V40	AATF_BGKLV13_13_GGCTAC_L002_R1_001.fastq.gz,AATF_BGKLV13_13_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	13470
AATF_BGKLV13_13_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	772					GRCh38	V40	AATF_BGKLV13_13/Aligned.sortedByCoord.out.bam		ENCORE2	13522
AATF_BGKLV13_13_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	772					GRCh38	V40	AATF_BGKLV13_13/Aligned.sortedByCoord.out.bam		ENCORE2	13574
AATF_BGKLV13_13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	772					GRCh38	V40	AATF_BGKLV13_13/Aligned.sortedByCoord.out.bam		ENCORE2	13626
AATF_BGKLV13_13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	772					GRCh38	V40	AATF_BGKLV13_13/Aligned.sortedByCoord.out.bam		ENCORE2	13678
AATF_BGKLV13_13_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	772					GRCh38	V40	AATF_BGKLV13_13_GGCTAC_L002_R1_001.fastq.gz,AATF_BGKLV13_13_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	13730
AATF_BGKLV13_14_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	773	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13367
AATF_BGKLV13_14_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	773	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13419
AATF_BGKLV13_14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	773					GRCh38	V40	AATF_BGKLV13_14_CTTGTA_L002_R1_001.fastq.gz,AATF_BGKLV13_14_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	13471
AATF_BGKLV13_14_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	773					GRCh38	V40	AATF_BGKLV13_14/Aligned.sortedByCoord.out.bam		ENCORE2	13523
AATF_BGKLV13_14_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	773					GRCh38	V40	AATF_BGKLV13_14/Aligned.sortedByCoord.out.bam		ENCORE2	13575
AATF_BGKLV13_14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	773					GRCh38	V40	AATF_BGKLV13_14/Aligned.sortedByCoord.out.bam		ENCORE2	13627
AATF_BGKLV13_14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	773					GRCh38	V40	AATF_BGKLV13_14/Aligned.sortedByCoord.out.bam		ENCORE2	13679
AATF_BGKLV13_14_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	773					GRCh38	V40	AATF_BGKLV13_14_CTTGTA_L002_R1_001.fastq.gz,AATF_BGKLV13_14_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	13731