AHCYL2 RNA-Seq in K562

General Information


RBP	AHCYL2
Cell_Line	K562
Method	CRISPR
Exp_Name	AHCYL2-BGKcLV26-K562
ENCODE_series_ID	ENCSR555AEQ
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR700JXJ
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	AHCYL2-BGKcLV26-17
Rep2	AHCYL2-BGKcLV26-18
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	75.5
Rep2_qPCR	74.1
Rep1_WB	78.1
Rep2_WB	85.3
Antibody Cat#	A300-262A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB809CIX
Status	Released
Project	ENCODE4
ID	787

Experiment Information (Status: Released)

	BGKcLV26-17	BGKcLV26-18
idx	870	871
TRCN#_or_BGC#	BGC#0000601	BGC#0000601
shRNA_or_gRNA_sequence	CCCCGACGGCACCGTCACCG	CCCCGACGGCACCGTCACCG
PAM	AGG	AGG
Name	AHCYL2_93	AHCYL2_93
Sample_ID	BGKcLV26-17	BGKcLV26-18
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	AHCYL2	AHCYL2
qPCR_result	75.5	74.1
Ave_qPCR	74.8
RT-qPCR_primer-F	gggtcgctataagcaggatg
RT-qPCR_primer-R	gtcaagtgggcatcaaaggt
protein_conc	3981	4238
WB_result	78.1	85.3
Ave_WB	81.7
WB_DONE_date	5/21/21	jess
MW	67KD+I348
IP	Rabbit / I
antibody_Cat#	A300-262A	LOT# 2
Antibody DCC ID	ENCAB809CIX	10/22/21
submitted_to_DCC_date
Rep1_TPM	3.7	0
Rep2_TPM	4.6	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5002	5003

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AHCYL2	Product_ID: A300-262A Lot_ID: 2 Source: Bethyl Labs Target Name: AHCYL2-human

Experiment Status

	BGKcLV26-17	BGKcLV26-18
Sample_ID	BGKcLV26-17	BGKcLV26-18
Sample Name
Sample Name	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-18
RBP	AHCYL2	AHCYL2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9755	9756

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-17	BGKcLV26-18
Sample #	13	14
Sample Name	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-18
Sample_Name_Alias
Index Well Position	E02	F02
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	276	279
Peak_Molarity	50.80	57.40
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/E2.png	DNA_Library_set48-49/set1/F2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/E2.png	RNA_Library_set48-49/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-17	BGKcLV26-18
RBP	AHCYL2	AHCYL2
Batch_ID	BGKcLV26	BGKcLV26
WB_result	78.100	85.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1572	1573

Sequencing Information

	BGKcLV26-17	BGKcLV26-18
Sample_ID	BGKcLV26-17	BGKcLV26-18
Sample Name	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-18
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	88,957,416	74,898,620
total_aligned_reads	79,234,862	67,397,542
unique_aligned_reads	72,428,994	61,669,162
percent_uniqueAligned	0.81420	0.82337
correlation_replicates	0.999345	0.999345
spikein_reads	40,368	25,558
percent_spikeins	0.00045	0.00034
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1749	1750

Data Submission Information

	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-18	BGKcLV26-18	BGKcLV26-18	BGKcLV26-18
ENCODE_alias	brenton-graveley:AHCYL2-BGKcLV26	brenton-graveley:AHCYL2-BGKcLV26-17	brenton-graveley:L-AHCYL2-BGKcLV26-17	brenton-graveley:AHCYL2-BGKcLV26-17_S19_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AHCYL2-BGKcLV26-17_S19_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AHCYL2-BGKcLV26-K562	brenton-graveley:AHCYL2-BGKcLV26-18	brenton-graveley:L-AHCYL2-BGKcLV26-18	brenton-graveley:AHCYL2-BGKcLV26-18_S20_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AHCYL2-BGKcLV26-18_S20_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR700JXJ	ENCBS898HTY	ENCLB429ENQ	ENCFF978JZA	ENCFF928GCT	ENCSR555AEQ	ENCBS082OUT	ENCLB678YKG	ENCFF166CBH	ENCFF243RWT
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	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-17	BGKcLV26-18	BGKcLV26-18	BGKcLV26-18	BGKcLV26-18
Sample Name	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-17	AHCYL2-BGKcLV26-18	AHCYL2-BGKcLV26-18	AHCYL2-BGKcLV26-18	AHCYL2-BGKcLV26-18
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		AHCYL2-BGKcLV26-17.pdf	L-AHCYL2-BGKcLV26-17.pdf				AHCYL2-BGKcLV26-18.pdf	L-AHCYL2-BGKcLV26-18.pdf
ID	3452	3538	3672	3806	3940	7075	3539	3673	3807	3941

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
AHCYL2-BGKcLV26-17_S19_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1749	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	3842
AHCYL2-BGKcLV26-17_S19_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1749	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	3892
AHCYL2-BGKcLV26-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1749					GRCh38	V40	AHCYL2-BGKcLV26-17_S19_L003_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGKcLV26-17_S19_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25529
AHCYL2-BGKcLV26-17_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1749					GRCh38	V40	AHCYL2-BGKcLV26-17_S19_L003_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGKcLV26-17_S19_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25579
AHCYL2-BGKcLV26-17_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	1749					GRCh38	V40	AHCYL2-BGKcLV26-17/Aligned.sortedByCoord.out.bam		ENCORE2	26545
AHCYL2-BGKcLV26-17_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	1749					GRCh38	V40	AHCYL2-BGKcLV26-17/Aligned.sortedByCoord.out.bam		ENCORE2	26595
AHCYL2-BGKcLV26-17_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	1749					GRCh38	V40	AHCYL2-BGKcLV26-17/Aligned.sortedByCoord.out.bam		ENCORE2	26645
AHCYL2-BGKcLV26-17_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	1749					GRCh38	V40	AHCYL2-BGKcLV26-17/Aligned.sortedByCoord.out.bam		ENCORE2	26695
AHCYL2-BGKcLV26-18_S20_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1750	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	3843
AHCYL2-BGKcLV26-18_S20_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1750	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	3893
AHCYL2-BGKcLV26-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1750					GRCh38	V40	AHCYL2-BGKcLV26-18_S20_L003_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGKcLV26-18_S20_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25530
AHCYL2-BGKcLV26-18_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1750					GRCh38	V40	AHCYL2-BGKcLV26-18_S20_L003_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGKcLV26-18_S20_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25580
AHCYL2-BGKcLV26-18_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	1750					GRCh38	V40	AHCYL2-BGKcLV26-18/Aligned.sortedByCoord.out.bam		ENCORE2	26546
AHCYL2-BGKcLV26-18_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	1750					GRCh38	V40	AHCYL2-BGKcLV26-18/Aligned.sortedByCoord.out.bam		ENCORE2	26596
AHCYL2-BGKcLV26-18_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	1750					GRCh38	V40	AHCYL2-BGKcLV26-18/Aligned.sortedByCoord.out.bam		ENCORE2	26646
AHCYL2-BGKcLV26-18_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	1750					GRCh38	V40	AHCYL2-BGKcLV26-18/Aligned.sortedByCoord.out.bam		ENCORE2	26696