AHCYL2 RNA-Seq in HepG2

General Information


RBP	AHCYL2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	AHCYL2-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR975NGU
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR363NMO
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	AHCYL2-BGHcLV25-21
Rep2	AHCYL2-BGHcLV25-22
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	70.2
Rep2_WB	67.8
Antibody Cat#	A300-262A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB809CIX
Status	Released
Project	ENCODE4
ID	18

Experiment Information (Status: Released)

	BGHcLV25-21	BGHcLV25-22
idx	728	729
TRCN#_or_BGC#	BGC#0000602	BGC#0000602
shRNA_or_gRNA_sequence	TAGTTGCGACTCCGCCTCGG	TAGTTGCGACTCCGCCTCGG
PAM	AGG	AGG
Name	AHCYL2_96	AHCYL2_96
Sample_ID	BGHcLV25-21	BGHcLV25-22
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	AHCYL2	AHCYL2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gggtcgctataagcaggatg
RT-qPCR_primer-R	gtcaagtgggcatcaaaggt
protein_conc	6347	5660
WB_result	70.2	67.8
Ave_WB	69.0
WB_DONE_date	5/21/21	JESS
MW	67KD
IP	Rabbit / I
antibody_Cat#	A300-262A	LOT# 2
Antibody DCC ID	ENCAB809CIX
submitted_to_DCC_date	10/26/21
Rep1_TPM	6	0
Rep2_TPM	7	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6887	6888

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

	BGHcLV25-21	BGHcLV25-22
Sample_ID	BGHcLV25-21	BGHcLV25-22
Sample Name
Sample Name	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-22
RBP	AHCYL2	AHCYL2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7841	7842

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-21	BGHcLV25-22
Sample #	39	40
Sample Name	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-22
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	338	291
Peak_Molarity	55.80	55.40
libSampleQC_DNA_Well	DNA_Library_set47/set1/G8.png	DNA_Library_set47/set1/H8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set47/set1/G5.png	RNA_Library_set47/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-21	BGHcLV25-22
RBP	AHCYL2	AHCYL2
Batch_ID	BGHcLV25	BGHcLV25
WB_result	70.200	67.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1502	1503

Sequencing Information

	BGHcLV25-21	BGHcLV25-22
Sample_ID	BGHcLV25-21	BGHcLV25-22
Sample Name	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-22
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	151,013,448	127,863,078
total_aligned_reads	138,737,868	116,350,858
unique_aligned_reads	130,659,570	109,372,452
percent_uniqueAligned	0.86522	0.85539
correlation_replicates	0.998495	0.998495
spikein_reads	40,284	35,978
percent_spikeins	0.00027	0.00028
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	584	585

Data Submission Information

	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-22	BGHcLV25-22	BGHcLV25-22	BGHcLV25-22
ENCODE_alias	brenton-graveley:AHCYL2-BGHcLV25	brenton-graveley:AHCYL2-BGHcLV25-21	brenton-graveley:L-AHCYL2-BGHcLV25-21	brenton-graveley:AHCYL2-BGHcLV25-21_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AHCYL2-BGHcLV25-21_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AHCYL2-BGHcLV25-HepG2	brenton-graveley:AHCYL2-BGHcLV25-22	brenton-graveley:L-AHCYL2-BGHcLV25-22	brenton-graveley:AHCYL2-BGHcLV25-22_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AHCYL2-BGHcLV25-22_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR363NMO	ENCBS060QNZ	ENCLB572CNO	ENCFF980MOO	ENCFF354FXT	ENCSR975NGU	ENCBS617TDS	ENCLB617BGA	ENCFF964BDA	ENCFF572EAM
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	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-21	BGHcLV25-22	BGHcLV25-22	BGHcLV25-22	BGHcLV25-22
Sample Name	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-21	AHCYL2-BGHcLV25-22	AHCYL2-BGHcLV25-22	AHCYL2-BGHcLV25-22	AHCYL2-BGHcLV25-22
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		AHCYL2-BGHcLV25-21.pdf	L-AHCYL2-BGHcLV25-21.pdf				AHCYL2-BGHcLV25-22.pdf	L-AHCYL2-BGHcLV25-22.pdf
ID	3254	3295	3339	3383	3427	7074	3296	3340	3384	3428

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-BGHcLV25-21_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	584	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3704
AHCYL2-BGHcLV25-21_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	584	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3750
AHCYL2-BGHcLV25-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	584					GRCh38	V40	AHCYL2-BGHcLV25-21_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGHcLV25-21_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25393
AHCYL2-BGHcLV25-21_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	584					GRCh38	V40	AHCYL2-BGHcLV25-21_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGHcLV25-21_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25437
AHCYL2-BGHcLV25-21_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	584					GRCh38	V40	AHCYL2-BGHcLV25-21/Aligned.sortedByCoord.out.bam		ENCORE2	26269
AHCYL2-BGHcLV25-21_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	584					GRCh38	V40	AHCYL2-BGHcLV25-21/Aligned.sortedByCoord.out.bam		ENCORE2	26313
AHCYL2-BGHcLV25-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	584					GRCh38	V40	AHCYL2-BGHcLV25-21/Aligned.sortedByCoord.out.bam		ENCORE2	26357
AHCYL2-BGHcLV25-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	584					GRCh38	V40	AHCYL2-BGHcLV25-21/Aligned.sortedByCoord.out.bam		ENCORE2	26401
AHCYL2-BGHcLV25-22_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	585	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3705
AHCYL2-BGHcLV25-22_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	585	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3751
AHCYL2-BGHcLV25-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	585					GRCh38	V40	AHCYL2-BGHcLV25-22_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGHcLV25-22_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25394
AHCYL2-BGHcLV25-22_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	585					GRCh38	V40	AHCYL2-BGHcLV25-22_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz,AHCYL2-BGHcLV25-22_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25438
AHCYL2-BGHcLV25-22_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	585					GRCh38	V40	AHCYL2-BGHcLV25-22/Aligned.sortedByCoord.out.bam		ENCORE2	26270
AHCYL2-BGHcLV25-22_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	585					GRCh38	V40	AHCYL2-BGHcLV25-22/Aligned.sortedByCoord.out.bam		ENCORE2	26314
AHCYL2-BGHcLV25-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	585					GRCh38	V40	AHCYL2-BGHcLV25-22/Aligned.sortedByCoord.out.bam		ENCORE2	26358
AHCYL2-BGHcLV25-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	585					GRCh38	V40	AHCYL2-BGHcLV25-22/Aligned.sortedByCoord.out.bam		ENCORE2	26402