ADD3 RNA-Seq in HepG2

General Information


RBP	ADD3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ADD3-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR204GIE
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR558DZW
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	ADD3-BGHcLV25-13
Rep2	ADD3-BGHcLV25-14
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR	51.2
Rep2_qPCR	50.1
Rep1_WB	98.7
Rep2_WB	97.9
Antibody Cat#	A303-715A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB314ANI
Status	Released
Project	ENCODE4
ID	15

Experiment Information (Status: Released)

	BGHcLV25-13	BGHcLV25-13	BGHcLV25-14	BGHcLV25-14
idx	720	0	721	0
TRCN#_or_BGC#	BGC#0000592	BGC#0000592	BGC#0000592	BGC#0000592
shRNA_or_gRNA_sequence	TGGCACTGTATCGTCTTCAA	TGGCACTGTATCGTCTTCAA	TGGCACTGTATCGTCTTCAA	TGGCACTGTATCGTCTTCAA
PAM	AGG	AGG	AGG	AGG
Name	ADD3_87	ADD3_87	ADD3_87	ADD3_87
Sample_ID	BGHcLV25-13	BGHcLV25-13	BGHcLV25-14	BGHcLV25-14
transduction_Date	2/18/21	2/18/21	2/18/21	2/18/21
days	D6	D6	D6	D6
RBP_name	ADD3	ADD3	ADD3	ADD3
qPCR_result	51.2	51.2	50.1	50.1
Ave_qPCR	50.7	50.7
RT-qPCR_primer-F	ttcccatcaaaaatggaagg	ttcccatcaaaaatggaagg
RT-qPCR_primer-R	acagttgctgggatttccac	acagttgctgggatttccac
protein_conc	6102	6102	5870	5870
WB_result	98.7	no clear band on the position	97.9
Ave_WB	98.3
WB_DONE_date	5/26/21	4/5/22	JESS
MW	79KD	79KD
IP	Rabbit / I
antibody_Cat#	A303-715A	A303-716A	LOT# 1
Antibody DCC ID	ENCAB314ANI
submitted_to_DCC_date	10/26/21
Rep1_TPM	48	0	0	0
Rep2_TPM	57	0	0	0
Action	Ready		Ready
Library_start_date	06/16/21		06/16/21
repeat_library
Note
ID	6875	6877	6876	6878

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ADD3	Product_ID: A303-715A Lot_ID: 1 Source: Bethyl Labs Target Name: ADD3-human

Experiment Status

	BGHcLV25-13	BGHcLV25-14
Sample_ID	BGHcLV25-13	BGHcLV25-14
Sample Name
Sample Name	ADD3-BGHcLV25-13	ADD3-BGHcLV25-14
RBP	ADD3	ADD3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7835	7836

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-13	BGHcLV25-14
Sample #	33	34
Sample Name	ADD3-BGHcLV25-13	ADD3-BGHcLV25-14
Sample_Name_Alias
Index Well Position	A11	B11
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	310	302
Peak_Molarity	63.80	76.50
libSampleQC_DNA_Well	DNA_Library_set47/set1/A8.png	DNA_Library_set47/set1/B8.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set47/set1/A5.png	RNA_Library_set47/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-13	BGHcLV25-14
RBP	ADD3	ADD3
Batch_ID	BGHcLV25	BGHcLV25
WB_result	98.700	97.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1496	1497

Sequencing Information

	BGHcLV25-13	BGHcLV25-14
Sample_ID	BGHcLV25-13	BGHcLV25-14
Sample Name	ADD3-BGHcLV25-13	ADD3-BGHcLV25-14
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	120,874,542	135,045,368
total_aligned_reads	110,912,008	125,506,544
unique_aligned_reads	104,538,002	118,247,960
percent_uniqueAligned	0.86485	0.87562
correlation_replicates	0.992691	0.992691
spikein_reads	60,234	50,534
percent_spikeins	0.00050	0.00037
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	578	579

Data Submission Information

	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-14	BGHcLV25-14	BGHcLV25-14	BGHcLV25-14
ENCODE_alias	brenton-graveley:ADD3-BGHcLV25	brenton-graveley:ADD3-BGHcLV25-13	brenton-graveley:L-ADD3-BGHcLV25-13	brenton-graveley:ADD3-BGHcLV25-13_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADD3-BGHcLV25-13_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADD3-BGHcLV25-HepG2	brenton-graveley:ADD3-BGHcLV25-14	brenton-graveley:L-ADD3-BGHcLV25-14	brenton-graveley:ADD3-BGHcLV25-14_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADD3-BGHcLV25-14_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR558DZW	ENCBS914PTZ	ENCLB049DGV	ENCFF381ARB	ENCFF693UNM	ENCSR204GIE	ENCBS605JYS	ENCLB188QWO	ENCFF391PRZ	ENCFF901MQH
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	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-13	BGHcLV25-14	BGHcLV25-14	BGHcLV25-14	BGHcLV25-14
Sample Name	ADD3-BGHcLV25-13	ADD3-BGHcLV25-13	ADD3-BGHcLV25-13	ADD3-BGHcLV25-13	ADD3-BGHcLV25-13	ADD3-BGHcLV25-13	ADD3-BGHcLV25-14	ADD3-BGHcLV25-14	ADD3-BGHcLV25-14	ADD3-BGHcLV25-14
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		ADD3-BGHcLV25-13.pdf	L-ADD3-BGHcLV25-13.pdf				ADD3-BGHcLV25-14.pdf	L-ADD3-BGHcLV25-14.pdf
ID	3251	3289	3333	3377	3421	7069	3290	3334	3378	3422

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
ADD3-BGHcLV25-13_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	578	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	3698
ADD3-BGHcLV25-13_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	578	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	3744
ADD3-BGHcLV25-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	578					GRCh38	V40	ADD3-BGHcLV25-13_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADD3-BGHcLV25-13_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25387
ADD3-BGHcLV25-13_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	578					GRCh38	V40	ADD3-BGHcLV25-13_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADD3-BGHcLV25-13_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25431
ADD3-BGHcLV25-13_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	578					GRCh38	V40	ADD3-BGHcLV25-13/Aligned.sortedByCoord.out.bam		ENCORE2	26263
ADD3-BGHcLV25-13_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	578					GRCh38	V40	ADD3-BGHcLV25-13/Aligned.sortedByCoord.out.bam		ENCORE2	26307
ADD3-BGHcLV25-13_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	578					GRCh38	V40	ADD3-BGHcLV25-13/Aligned.sortedByCoord.out.bam		ENCORE2	26351
ADD3-BGHcLV25-13_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	578					GRCh38	V40	ADD3-BGHcLV25-13/Aligned.sortedByCoord.out.bam		ENCORE2	26395
ADD3-BGHcLV25-14_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	579	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	3699
ADD3-BGHcLV25-14_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	579	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	3745
ADD3-BGHcLV25-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	579					GRCh38	V40	ADD3-BGHcLV25-14_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADD3-BGHcLV25-14_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25388
ADD3-BGHcLV25-14_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	579					GRCh38	V40	ADD3-BGHcLV25-14_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADD3-BGHcLV25-14_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25432
ADD3-BGHcLV25-14_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	579					GRCh38	V40	ADD3-BGHcLV25-14/Aligned.sortedByCoord.out.bam		ENCORE2	26264
ADD3-BGHcLV25-14_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	579					GRCh38	V40	ADD3-BGHcLV25-14/Aligned.sortedByCoord.out.bam		ENCORE2	26308
ADD3-BGHcLV25-14_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	579					GRCh38	V40	ADD3-BGHcLV25-14/Aligned.sortedByCoord.out.bam		ENCORE2	26352
ADD3-BGHcLV25-14_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	579					GRCh38	V40	ADD3-BGHcLV25-14/Aligned.sortedByCoord.out.bam		ENCORE2	26396