FASTKD2 RNA-Seq in K562

General Information


RBP	FASTKD2
Cell_Line	K562
Method	shRNA
Exp_Name	FASTKD2-BGKLV13-K562
ENCODE_series_ID	ENCSR610SZF
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR608IAI
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	FASTKD2_BGKLV13_53
Rep2	FASTKD2_BGKLV13_54
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	60.8
Rep2_qPCR	68.2
Rep1_WB	46.9
Rep2_WB	51.6
Antibody Cat#	A303-788A
Antibody Lot#	A303-788A
Antibody DCC ID	ENCAB541LFT
Status	Released
Project	ENCODE3
ID	376

Experiment Information (Status: Released)

	BGKLV13-53	BGKLV13-54
idx	188	189
TRCN#_or_BGC#	TRCN0000145126	TRCN0000145126
shRNA_or_gRNA_sequence	GCTTTCAAACAAAGGGCATAA	GCTTTCAAACAAAGGGCATAA
PAM
Name	FASTKD2	FASTKD2
Sample_ID	BGKLV13-53	BGKLV13-54
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	FASTKD2	FASTKD2
qPCR_result	60.8	68.2
Ave_qPCR	64.5
RT-qPCR_primer-F	GCATTTGAATGCAATGGGT
RT-qPCR_primer-R	TGTGACTGCATCTTCCATCTCT
protein_conc	2075	2100
WB_result	46.9	51.6
Ave_WB	49.3
WB_DONE_date	7/2/2014
MW	81kDa
IP	1MW	1MW
antibody_Cat#	A303-788A	A303-788A
Antibody DCC ID	ENCAB541LFT	ENCAB541LFT
submitted_to_DCC_date	5/4/2015
Rep1_TPM	8.63226421	0
Rep2_TPM	4.31563641	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	207	208

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FASTKD2	Product_ID: A303-788A Lot_ID: 1 Source: Bethyl Labs Target Name: FASTKD2-human

Experiment Status

	BGKLV13-53	BGKLV13-54
Sample_ID	BGKLV13-53	BGKLV13-54
Sample Name	FASTKD2_BGKLV13_53	FASTKD2_BGKLV13_54
Sample Name	FASTKD2_BGKLV13_53	FASTKD2_BGKLV13_54
RBP	FASTKD2	FASTKD2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	450	451

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-53	BGKLV13-54
Sample #
Sample Name	FASTKD2-BGKLV13-53	FASTKD2-BGKLV13-54
Sample_Name_Alias	FASTKD2_BGKLV13_53	FASTKD2_BGKLV13_54
Index Well Position	S13	S14
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/F5.png	DNA_Library_LV13-14/set1/G5.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A2.png	RNA_Library_LV13-14-16/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-53	BGKLV13-54
RBP	FASTKD2	FASTKD2
Batch_ID	BGKLV13	BGKLV13
WB_result	46.900	51.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2156	2157

Sequencing Information

	BGKLV13-53	BGKLV13-54
Sample_ID	BGKLV13-53	BGKLV13-54
Sample Name	FASTKD2_BGKLV13_53	FASTKD2_BGKLV13_54
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	57,840,000	44,410,000
total_aligned_reads	54,085,022	41,733,598
unique_aligned_reads	49,947,474	38,428,928
percent_uniqueAligned	0.86355	0.86532
correlation_replicates	0.992588	0.992588
spikein_reads	289,228	153,650
percent_spikeins	0.00500	0.00346
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	798	799

Data Submission Information

	BGKLV13-53	BGKLV13-53
ENCODE_alias	brenton-graveley:FASTKD2_BGKLV13	brenton-graveley:FASTKD2-BGKLV13-K562
ENCODE_accession	ENCSR608IAI	ENCSR610SZF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-53	BGKLV13-53
Sample Name	FASTKD2_BGKLV13_53	FASTKD2_BGKLV13_53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2774	6710

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
FASTKD2_BGKLV13_53_AGTCAA_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	798	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13378
FASTKD2_BGKLV13_53_AGTCAA_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	798	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13430
FASTKD2_BGKLV13_53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	798					GRCh38	V40	FASTKD2_BGKLV13_53_AGTCAA_L006_R1_001.fastq.gz,FASTKD2_BGKLV13_53_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	13482
FASTKD2_BGKLV13_53_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	798					GRCh38	V40	FASTKD2_BGKLV13_53/Aligned.sortedByCoord.out.bam		ENCORE2	13534
FASTKD2_BGKLV13_53_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	798					GRCh38	V40	FASTKD2_BGKLV13_53/Aligned.sortedByCoord.out.bam		ENCORE2	13586
FASTKD2_BGKLV13_53_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	798					GRCh38	V40	FASTKD2_BGKLV13_53/Aligned.sortedByCoord.out.bam		ENCORE2	13638
FASTKD2_BGKLV13_53_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	798					GRCh38	V40	FASTKD2_BGKLV13_53/Aligned.sortedByCoord.out.bam		ENCORE2	13690
FASTKD2_BGKLV13_53_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	798					GRCh38	V40	FASTKD2_BGKLV13_53_AGTCAA_L006_R1_001.fastq.gz,FASTKD2_BGKLV13_53_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	13742
FASTKD2_BGKLV13_54_AGTTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	799	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13379
FASTKD2_BGKLV13_54_AGTTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	799	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13431
FASTKD2_BGKLV13_54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	799					GRCh38	V40	FASTKD2_BGKLV13_54_AGTTCC_L006_R1_001.fastq.gz,FASTKD2_BGKLV13_54_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	13483
FASTKD2_BGKLV13_54_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	799					GRCh38	V40	FASTKD2_BGKLV13_54/Aligned.sortedByCoord.out.bam		ENCORE2	13535
FASTKD2_BGKLV13_54_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	799					GRCh38	V40	FASTKD2_BGKLV13_54/Aligned.sortedByCoord.out.bam		ENCORE2	13587
FASTKD2_BGKLV13_54_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	799					GRCh38	V40	FASTKD2_BGKLV13_54/Aligned.sortedByCoord.out.bam		ENCORE2	13639
FASTKD2_BGKLV13_54_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	799					GRCh38	V40	FASTKD2_BGKLV13_54/Aligned.sortedByCoord.out.bam		ENCORE2	13691
FASTKD2_BGKLV13_54_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	799					GRCh38	V40	FASTKD2_BGKLV13_54_AGTTCC_L006_R1_001.fastq.gz,FASTKD2_BGKLV13_54_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	13743