TRA2A RNA-Seq in K562

General Information


RBP	TRA2A
Cell_Line	K562
Method	CRISPR
Exp_Name	TRA2A-BGKcLV11-K562
ENCODE_series_ID	ENCSR858ONP
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR564RKL
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	TRA2A-BGKcLV11-105
Rep2	TRA2A-BGKcLV11-106
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	25.0
Rep2_qPCR	0.0
Rep1_WB	84.9
Rep2_WB	88.9
Antibody Cat#	A303-779A
Antibody Lot#
Antibody DCC ID	ENCAB683DWW
Status	Released
Project	ENCODE4
ID	194

Experiment Information (Status: Released)

	BGKcLV11-105	BGKcLV11-106
idx	421	422
TRCN#_or_BGC#	BGC#0000155	BGC#0000155
shRNA_or_gRNA_sequence	CTCGTGTAAAATCGGAGAGC	CTCGTGTAAAATCGGAGAGC
PAM	AGG	AGG
Name	TRA2A_89F	TRA2A_89F
Sample_ID	BGKcLV11-105	BGKcLV11-106
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	TRA2A	TRA2A
qPCR_result	25.0	0.0
Ave_qPCR	12.5
RT-qPCR_primer-F	CGATCACCTTCTCCTTATTATAGTCG
RT-qPCR_primer-R	TCCTTAATTGCAACCATTCC
protein_conc	3184	3154
WB_result	84.9	88.9
Ave_WB	86.9
WB_DONE_date	9/27/18
MW	33 kDa
IP
antibody_Cat#	A303-779A
Antibody DCC ID	ENCAB683DWW
submitted_to_DCC_date	2/22/19
Rep1_TPM	87.6	0
Rep2_TPM	143.2	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4523	4524

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TRA2A	Product_ID: A303-779A Lot_ID: 1 Source: Bethyl Labs Target Name: TRA2A-human

Experiment Status

	BGKcLV11-105	BGKcLV11-106
Sample_ID	BGKcLV11-105	BGKcLV11-106
Sample Name	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-106
Sample Name	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-106
RBP	TRA2A	TRA2A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2697	2698

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-105	BGKcLV11-106
Sample #	25	26
Sample Name	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-106
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	2-A2	2-B2
Tecan	67.54	87.16
Tecan_date	2019-03-13	2019-03-13
Size_bp	292	290
Peak_Molarity	102.00	155.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/A4.png	DNA_Library_set42/set1/B4.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_set42/set1/A4.png	RNA_Library_set42/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-105	BGKcLV11-106
RBP	TRA2A	TRA2A
Batch_ID	BGKcLV11	BGKcLV11
WB_result	84.900	88.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	25	26

Sequencing Information

	BGKcLV11-105	BGKcLV11-106
Sample_ID	BGKcLV11-105	BGKcLV11-106
Sample Name	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-106
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	91,362,986	61,342,530
total_aligned_reads	89,451,842	58,987,580
unique_aligned_reads	80,357,262	53,320,746
percent_uniqueAligned	0.87954	0.86923
correlation_replicates	0.997657	0.997657
spikein_reads	186,206	98,594
percent_spikeins	0.00204	0.00161
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	75	76

Data Submission Information

	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-106	BGKcLV11-106	BGKcLV11-106	BGKcLV11-106
ENCODE_alias	brenton-graveley:TRA2A-BGKcLV11	brenton-graveley:TRA2A-BGKcLV11-105	brenton-graveley:L-TRA2A-BGKcLV11-105	brenton-graveley:TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:TRA2A-BGKcLV11-K562	brenton-graveley:TRA2A-BGKcLV11-106	brenton-graveley:L-TRA2A-BGKcLV11-106	brenton-graveley:TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR564RKL	ENCBS953RZD	ENCLB661EMQ	ENCFF068SYD	ENCFF471HGA	ENCSR858ONP	ENCBS114SKJ	ENCLB890GDZ	ENCFF849RIS	ENCFF562WVL
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	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-105	BGKcLV11-106	BGKcLV11-106	BGKcLV11-106	BGKcLV11-106
Sample Name	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-105	TRA2A-BGKcLV11-106	TRA2A-BGKcLV11-106	TRA2A-BGKcLV11-106	TRA2A-BGKcLV11-106
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
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		TRA2A-BGKcLV11-105.pdf	L-TRA2A-BGKcLV11-105.pdf				TRA2A-BGKcLV11-106.pdf	L-TRA2A-BGKcLV11-106.pdf
ID	773	841	923	1025	1107	7347	842	924	1026	1108

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
TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	75	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	407
TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	75	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	489
TRA2A-BGKcLV11-105_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	75					GRCh38	V40	TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23746
TRA2A-BGKcLV11-105_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	75					GRCh38	V40	TRA2A-BGKcLV11-105/Aligned.sortedByCoord.out.bam		ENCORE2	23828
TRA2A-BGKcLV11-105_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	75					GRCh38	V40	TRA2A-BGKcLV11-105/Aligned.sortedByCoord.out.bam		ENCORE2	23910
TRA2A-BGKcLV11-105_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	75					GRCh38	V40	TRA2A-BGKcLV11-105/Aligned.sortedByCoord.out.bam		ENCORE2	23992
TRA2A-BGKcLV11-105_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	75					GRCh38	V40	TRA2A-BGKcLV11-105/Aligned.sortedByCoord.out.bam		ENCORE2	24074
TRA2A-BGKcLV11-105_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	75					GRCh38	V40	TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRA2A-BGKcLV11-105_ACTAAGAT+AACCGCGG_HK3H2DSXX_S25_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24156
TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	76	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	408
TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	76	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	490
TRA2A-BGKcLV11-106_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	76					GRCh38	V40	TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23747
TRA2A-BGKcLV11-106_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	76					GRCh38	V40	TRA2A-BGKcLV11-106/Aligned.sortedByCoord.out.bam		ENCORE2	23829
TRA2A-BGKcLV11-106_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	76					GRCh38	V40	TRA2A-BGKcLV11-106/Aligned.sortedByCoord.out.bam		ENCORE2	23911
TRA2A-BGKcLV11-106_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	76					GRCh38	V40	TRA2A-BGKcLV11-106/Aligned.sortedByCoord.out.bam		ENCORE2	23993
TRA2A-BGKcLV11-106_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	76					GRCh38	V40	TRA2A-BGKcLV11-106/Aligned.sortedByCoord.out.bam		ENCORE2	24075
TRA2A-BGKcLV11-106_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	76					GRCh38	V40	TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRA2A-BGKcLV11-106_GTCGGAGC+GGTTATAA_HK3H2DSXX_S26_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24157