ETF1 RNA-Seq in K562

General Information


RBP	ETF1
Cell_Line	K562
Method	CRISPR
Exp_Name	ETF1-BGKcLV08-K562
ENCODE_series_ID	ENCSR656LJY
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR066ZMF
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	ETF1-BGKcLV08-33
Rep2	ETF1-BGKcLV08-34
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	76.4
Rep2_qPCR	82.5
Rep1_WB	55.8
Rep2_WB	53.6
Antibody Cat#	RN111PW
Antibody Lot#	RN111PW
Antibody DCC ID	ENCAB767NXE
Status	Released
Project	ENCODE4
ID	204

Experiment Information (Status: Released)

	BGKcLV08-33	BGKcLV08-34
idx	258	259
TRCN#_or_BGC#	BGC#0000121	BGC#0000121
shRNA_or_gRNA_sequence	AATGGTCTGGTTGTATACTG	AATGGTCTGGTTGTATACTG
PAM	TGG	TGG
Name	ETF1-79F	ETF1-79F
Sample_ID	BGKcLV08-33	BGKcLV08-34
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	ETF1	ETF1
qPCR_result	76.4	82.5
Ave_qPCR	79.5
RT-qPCR_primer-F	aaggatttggtggaattgga
RT-qPCR_primer-R	ttcatcgtctcctccttggt
protein_conc	3427	3229
WB_result	55.8	53.6
Ave_WB	54.7
WB_DONE_date	3/12/18	wes
MW	49kDa
IP
antibody_Cat#	RN111PW	RN111PW
Antibody DCC ID	ENCAB767NXE
submitted_to_DCC_date	9/6/18
Rep1_TPM	61.5	0
Rep2_TPM	36.3	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4358	4359

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ETF1	Product_ID: RN111PW Lot_ID: 1 Source: MBLI Target Name: ETF1-human

Experiment Status

	BGKcLV08-33	BGKcLV08-34
Sample_ID	BGKcLV08-33	BGKcLV08-34
Sample Name
Sample Name	ETF1-BGKcLV08-33	ETF1-BGKcLV08-34
RBP	ETF1	ETF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6179	6180

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-33	BGKcLV08-34
Sample #	15	16
Sample Name	ETF1-BGKcLV08-33	ETF1-BGKcLV08-34
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	277	274
Peak_Molarity	40.50	61.50
libSampleQC_DNA_Well	DNA_Library_set41/set2/G2.png	DNA_Library_set41/set2/H2.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set41/set1/G2.png	RNA_Library_set41/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-33	BGKcLV08-34
RBP	ETF1	ETF1
Batch_ID	BGKcLV08	BGKcLV08
WB_result	55.800	53.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	865	866

Sequencing Information

	BGKcLV08-33	BGKcLV08-34
Sample_ID	BGKcLV08-33	BGKcLV08-34
Sample Name	ETF1-BGKcLV08-33	ETF1-BGKcLV08-34
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	86,229,620	72,122,920
total_aligned_reads	80,251,646	70,730,146
unique_aligned_reads	72,414,996	63,936,690
percent_uniqueAligned	0.83979	0.88650
correlation_replicates	0.990759	0.990759
spikein_reads	131,972	109,414
percent_spikeins	0.00153	0.00152
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	271	272

Data Submission Information

	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-34	BGKcLV08-34	BGKcLV08-34	BGKcLV08-34
ENCODE_alias	brenton-graveley:ETF1-BGKcLV08	brenton-graveley:ETF1-BGKcLV08-33	brenton-graveley:L-ETF1-BGKcLV08-33	brenton-graveley:ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ETF1-BGKcLV08-K562	brenton-graveley:ETF1-BGKcLV08-34	brenton-graveley:L-ETF1-BGKcLV08-34	brenton-graveley:ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR066ZMF	ENCBS164XZU	ENCLB805CGQ	ENCFF280YVB	ENCFF290MFJ	ENCSR656LJY	ENCBS355TWU	ENCLB725NNA	ENCFF997XOS	ENCFF252VIN
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-33	BGKcLV08-34	BGKcLV08-34	BGKcLV08-34	BGKcLV08-34
Sample Name	ETF1-BGKcLV08-33	ETF1-BGKcLV08-33	ETF1-BGKcLV08-33	ETF1-BGKcLV08-33	ETF1-BGKcLV08-33	ETF1-BGKcLV08-33	ETF1-BGKcLV08-34	ETF1-BGKcLV08-34	ETF1-BGKcLV08-34	ETF1-BGKcLV08-34
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		ETF1-BGKcLV08-33.pdf	L-ETF1-BGKcLV08-33.pdf				ETF1-BGKcLV08-34.pdf	L-ETF1-BGKcLV08-34.pdf
ID	1126	1172	1242	1312	1382	7215	1173	1243	1313	1383

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	271				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	519
ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	271				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	589
ETF1-BGKcLV08-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	271	GRCh38	V40	ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26757
ETF1-BGKcLV08-33_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	271	GRCh38	V40	ETF1-BGKcLV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	26827
ETF1-BGKcLV08-33_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	271	GRCh38	V40	ETF1-BGKcLV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	26897
ETF1-BGKcLV08-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	271	GRCh38	V40	ETF1-BGKcLV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	26967
ETF1-BGKcLV08-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	271	GRCh38	V40	ETF1-BGKcLV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	27037
ETF1-BGKcLV08-33_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	271	GRCh38	V40	ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ETF1-BGKcLV08-33_GGCTTAAG+TCGTGACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27107
ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	272				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	520
ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	272				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	590
ETF1-BGKcLV08-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	272	GRCh38	V40	ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26758
ETF1-BGKcLV08-34_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	272	GRCh38	V40	ETF1-BGKcLV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	26828
ETF1-BGKcLV08-34_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	272	GRCh38	V40	ETF1-BGKcLV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	26898
ETF1-BGKcLV08-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	272	GRCh38	V40	ETF1-BGKcLV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	26968
ETF1-BGKcLV08-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	272	GRCh38	V40	ETF1-BGKcLV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	27038
ETF1-BGKcLV08-34_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	272	GRCh38	V40	ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ETF1-BGKcLV08-34_AATCCGGA+CTACAGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27108