ADK RNA-Seq in K562

General Information


RBP	ADK
Cell_Line	K562
Method	CRISPR
Exp_Name	ADK-BGKcLV26-K562
ENCODE_series_ID	ENCSR831IJN
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR812JYP
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ADK-BGKcLV26-11
Rep2	ADK-BGKcLV26-12
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	47.6
Rep2_qPCR	47.1
Rep1_WB	61.3
Rep2_WB	69.9
Antibody Cat#	A304-280A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB355LKV
Status	Released
Project	ENCODE4
ID	785

Experiment Information (Status: Released)

	BGKcLV26-11	BGKcLV26-12
idx	864	865
TRCN#_or_BGC#	BGC#0000596	BGC#0000596
shRNA_or_gRNA_sequence	CGTAGTAATGAGCATCCACA	CGTAGTAATGAGCATCCACA
PAM	tgg	tgg
Name	ADK_93	ADK_93
Sample_ID	BGKcLV26-11	BGKcLV26-12
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	ADK	ADK
qPCR_result	47.6	47.1
Ave_qPCR	47.3
RT-qPCR_primer-F	atgagcagccaacaggaact
RT-qPCR_primer-R	taacaattggcagcagcaag
protein_conc	4219	4326
WB_result	61.3	69.9
Ave_WB	65.6
WB_DONE_date	4/14/21
MW	40.5KD
IP	Rabbit / I
antibody_Cat#	A304-280A	LOT# 1
Antibody DCC ID	ENCAB355LKV	10/22/21
submitted_to_DCC_date
Rep1_TPM	60.9	0
Rep2_TPM	59.1	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	4996	4997

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ADK	Product_ID: A304-280A Lot_ID: 1 Source: Bethyl Labs Target Name: ADK-human

Experiment Status

	BGKcLV26-11	BGKcLV26-12
Sample_ID	BGKcLV26-11	BGKcLV26-12
Sample Name
Sample Name	ADK-BGKcLV26-11	ADK-BGKcLV26-12
RBP	ADK	ADK
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9751	9752

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-11	BGKcLV26-12
Sample #	9	10
Sample Name	ADK-BGKcLV26-11	ADK-BGKcLV26-12
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	285	291
Peak_Molarity	79.50	74.30
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/A2.png	DNA_Library_set48-49/set1/B2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/A2.png	RNA_Library_set48-49/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-11	BGKcLV26-12
RBP	ADK	ADK
Batch_ID	BGKcLV26	BGKcLV26
WB_result	61.300	69.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1568	1569

Sequencing Information

	BGKcLV26-11	BGKcLV26-12
Sample_ID	BGKcLV26-11	BGKcLV26-12
Sample Name	ADK-BGKcLV26-11	ADK-BGKcLV26-12
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	109,563,658	99,652,520
total_aligned_reads	97,095,730	84,811,176
unique_aligned_reads	88,407,254	77,047,114
percent_uniqueAligned	0.80690	0.77316
correlation_replicates	0.999655	0.999655
spikein_reads	63,840	44,522
percent_spikeins	0.00058	0.00045
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1745	1746

Data Submission Information

	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-12	BGKcLV26-12	BGKcLV26-12	BGKcLV26-12
ENCODE_alias	brenton-graveley:ADK-BGKcLV26	brenton-graveley:ADK-BGKcLV26-11	brenton-graveley:L-ADK-BGKcLV26-11	brenton-graveley:ADK-BGKcLV26-11_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADK-BGKcLV26-11_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADK-BGKcLV26-K562	brenton-graveley:ADK-BGKcLV26-12	brenton-graveley:L-ADK-BGKcLV26-12	brenton-graveley:ADK-BGKcLV26-12_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADK-BGKcLV26-12_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR812JYP	ENCBS502VJO	ENCLB613FJN	ENCFF588ACW	ENCFF714YPD	ENCSR831IJN	ENCBS718XWF	ENCLB861EYW	ENCFF280VEU	ENCFF086RNI
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	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-11	BGKcLV26-12	BGKcLV26-12	BGKcLV26-12	BGKcLV26-12
Sample Name	ADK-BGKcLV26-11	ADK-BGKcLV26-11	ADK-BGKcLV26-11	ADK-BGKcLV26-11	ADK-BGKcLV26-11	ADK-BGKcLV26-11	ADK-BGKcLV26-12	ADK-BGKcLV26-12	ADK-BGKcLV26-12	ADK-BGKcLV26-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		ADK-BGKcLV26-11.pdf	L-ADK-BGKcLV26-11.pdf				ADK-BGKcLV26-12.pdf	L-ADK-BGKcLV26-12.pdf
ID	3450	3534	3668	3802	3936	7071	3535	3669	3803	3937

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
ADK-BGKcLV26-11_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1745	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3838
ADK-BGKcLV26-11_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1745	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3888
ADK-BGKcLV26-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1745					GRCh38	V40	ADK-BGKcLV26-11_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGKcLV26-11_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25525
ADK-BGKcLV26-11_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1745					GRCh38	V40	ADK-BGKcLV26-11_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGKcLV26-11_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25575
ADK-BGKcLV26-11_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1745					GRCh38	V40	ADK-BGKcLV26-11/Aligned.sortedByCoord.out.bam		ENCORE2	26541
ADK-BGKcLV26-11_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1745					GRCh38	V40	ADK-BGKcLV26-11/Aligned.sortedByCoord.out.bam		ENCORE2	26591
ADK-BGKcLV26-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1745					GRCh38	V40	ADK-BGKcLV26-11/Aligned.sortedByCoord.out.bam		ENCORE2	26641
ADK-BGKcLV26-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1745					GRCh38	V40	ADK-BGKcLV26-11/Aligned.sortedByCoord.out.bam		ENCORE2	26691
ADK-BGKcLV26-12_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1746	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3839
ADK-BGKcLV26-12_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1746	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3889
ADK-BGKcLV26-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1746					GRCh38	V40	ADK-BGKcLV26-12_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGKcLV26-12_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25526
ADK-BGKcLV26-12_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1746					GRCh38	V40	ADK-BGKcLV26-12_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGKcLV26-12_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25576
ADK-BGKcLV26-12_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1746					GRCh38	V40	ADK-BGKcLV26-12/Aligned.sortedByCoord.out.bam		ENCORE2	26542
ADK-BGKcLV26-12_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1746					GRCh38	V40	ADK-BGKcLV26-12/Aligned.sortedByCoord.out.bam		ENCORE2	26592
ADK-BGKcLV26-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1746					GRCh38	V40	ADK-BGKcLV26-12/Aligned.sortedByCoord.out.bam		ENCORE2	26642
ADK-BGKcLV26-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1746					GRCh38	V40	ADK-BGKcLV26-12/Aligned.sortedByCoord.out.bam		ENCORE2	26692