ADK RNA-Seq in HepG2

General Information


RBP	ADK
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ADK-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR894BPS
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR924AVW
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	ADK-BGHcLV25-15
Rep2	ADK-BGHcLV25-16
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	87.8
Rep2_WB	90.9
Antibody Cat#	A304-280A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB355LKV
Status	Released
Project	ENCODE4
ID	16

Experiment Information (Status: Released)

	BGHcLV25-15	BGHcLV25-16
idx	722	723
TRCN#_or_BGC#	BGC#0000596	BGC#0000596
shRNA_or_gRNA_sequence	CGTAGTAATGAGCATCCACA	CGTAGTAATGAGCATCCACA
PAM	tgg	tgg
Name	ADK_93	ADK_93
Sample_ID	BGHcLV25-15	BGHcLV25-16
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	ADK	ADK
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5859	6492
WB_result	87.8	90.9
Ave_WB	89.4
WB_DONE_date	4/13/21
MW	40.5KD
IP	Rabbit / I
antibody_Cat#	A304-280A	LOT# 1
Antibody DCC ID	ENCAB355LKV
submitted_to_DCC_date	10/26/21
Rep1_TPM	46	0
Rep2_TPM	74	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6879	6880

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

	BGHcLV25-15	BGHcLV25-16
Sample_ID	BGHcLV25-15	BGHcLV25-16
Sample Name
Sample Name	ADK-BGHcLV25-15	ADK-BGHcLV25-16
RBP	ADK	ADK
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7837	7838

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-15	BGHcLV25-16
Sample #	35	36
Sample Name	ADK-BGHcLV25-15	ADK-BGHcLV25-16
Sample_Name_Alias
Index Well Position	C11	D11
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	311	345
Peak_Molarity	73.50	71.50
libSampleQC_DNA_Well	DNA_Library_set47/set1/C8.png	DNA_Library_set47/set1/D8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set47/set1/C5.png	RNA_Library_set47/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-15	BGHcLV25-16
RBP	ADK	ADK
Batch_ID	BGHcLV25	BGHcLV25
WB_result	87.800	90.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1498	1499

Sequencing Information

	BGHcLV25-15	BGHcLV25-16
Sample_ID	BGHcLV25-15	BGHcLV25-16
Sample Name	ADK-BGHcLV25-15	ADK-BGHcLV25-16
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	96,231,374	128,048,182
total_aligned_reads	89,759,194	120,278,780
unique_aligned_reads	84,589,712	113,336,448
percent_uniqueAligned	0.87902	0.88511
correlation_replicates	0.998746	0.998746
spikein_reads	30,488	26,246
percent_spikeins	0.00032	0.00020
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	580	581

Data Submission Information

	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-16	BGHcLV25-16	BGHcLV25-16	BGHcLV25-16
ENCODE_alias	brenton-graveley:ADK-BGHcLV25	brenton-graveley:ADK-BGHcLV25-15	brenton-graveley:L-ADK-BGHcLV25-15	brenton-graveley:ADK-BGHcLV25-15_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADK-BGHcLV25-15_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADK-BGHcLV25-HepG2	brenton-graveley:ADK-BGHcLV25-16	brenton-graveley:L-ADK-BGHcLV25-16	brenton-graveley:ADK-BGHcLV25-16_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADK-BGHcLV25-16_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR924AVW	ENCBS273CKO	ENCLB386CSX	ENCFF664KUH	ENCFF399SSW	ENCSR894BPS	ENCBS373FPT	ENCLB230AQZ	ENCFF443PRR	ENCFF499TJH
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	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-15	BGHcLV25-16	BGHcLV25-16	BGHcLV25-16	BGHcLV25-16
Sample Name	ADK-BGHcLV25-15	ADK-BGHcLV25-15	ADK-BGHcLV25-15	ADK-BGHcLV25-15	ADK-BGHcLV25-15	ADK-BGHcLV25-15	ADK-BGHcLV25-16	ADK-BGHcLV25-16	ADK-BGHcLV25-16	ADK-BGHcLV25-16
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-04	2022-02-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2022-02-04	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		ADK-BGHcLV25-15.pdf	L-ADK-BGHcLV25-15.pdf				ADK-BGHcLV25-16.pdf	L-ADK-BGHcLV25-16.pdf
ID	3252	3291	3335	3379	3423	7070	3292	3336	3380	3424

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-BGHcLV25-15_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	580	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	3700
ADK-BGHcLV25-15_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	580	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	3746
ADK-BGHcLV25-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	580					GRCh38	V40	ADK-BGHcLV25-15_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGHcLV25-15_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25389
ADK-BGHcLV25-15_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	580					GRCh38	V40	ADK-BGHcLV25-15_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGHcLV25-15_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25433
ADK-BGHcLV25-15_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	580					GRCh38	V40	ADK-BGHcLV25-15/Aligned.sortedByCoord.out.bam		ENCORE2	26265
ADK-BGHcLV25-15_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	580					GRCh38	V40	ADK-BGHcLV25-15/Aligned.sortedByCoord.out.bam		ENCORE2	26309
ADK-BGHcLV25-15_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	580					GRCh38	V40	ADK-BGHcLV25-15/Aligned.sortedByCoord.out.bam		ENCORE2	26353
ADK-BGHcLV25-15_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	580					GRCh38	V40	ADK-BGHcLV25-15/Aligned.sortedByCoord.out.bam		ENCORE2	26397
ADK-BGHcLV25-16_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	581	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	3701
ADK-BGHcLV25-16_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	581	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	3747
ADK-BGHcLV25-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	581					GRCh38	V40	ADK-BGHcLV25-16_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGHcLV25-16_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25390
ADK-BGHcLV25-16_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	581					GRCh38	V40	ADK-BGHcLV25-16_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADK-BGHcLV25-16_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25434
ADK-BGHcLV25-16_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	581					GRCh38	V40	ADK-BGHcLV25-16/Aligned.sortedByCoord.out.bam		ENCORE2	26266
ADK-BGHcLV25-16_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	581					GRCh38	V40	ADK-BGHcLV25-16/Aligned.sortedByCoord.out.bam		ENCORE2	26310
ADK-BGHcLV25-16_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	581					GRCh38	V40	ADK-BGHcLV25-16/Aligned.sortedByCoord.out.bam		ENCORE2	26354
ADK-BGHcLV25-16_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	581					GRCh38	V40	ADK-BGHcLV25-16/Aligned.sortedByCoord.out.bam		ENCORE2	26398