RTCB RNA-Seq in HepG2

General Information


RBP	RTCB
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RTCB-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR143VRA
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR726RTM
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	RTCB-BGHcLV31-17
Rep2	RTCB-BGHcLV31-18
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	74.6
Rep2_qPCR	73.2
Rep1_WB	70.4
Rep2_WB	75.7
Antibody Cat#	A305-078A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB377OYK
Status	Submitted
Project	ENCODE4
ID	920

Experiment Information (Status: Released)

	BGHcLV31-17	BGHcLV31-18
idx	933	934
TRCN#_or_BGC#	BGC#0000833	BGC#0000833
shRNA_or_gRNA_sequence	GTACTTACCACCACCTCGAC	GTACTTACCACCACCTCGAC
PAM	ACC	ACC
Name	RTCB_93	RTCB_93
Sample_ID	BGHcLV31-17	BGHcLV31-18
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	RTCB	RTCB
qPCR_result	74.6	73.2
Ave_qPCR	73.9
RT-qPCR_primer-F	tgatgctctggagaaattgatg
RT-qPCR_primer-R	attgccaatctgtttcatgg
protein_conc	3918	4485
WB_result	70.4	75.7
Ave_WB	73.1
WB_DONE_date	11/4/21
MW	55kd
IP
antibody_Cat#	A305-078A	LOT #1
Antibody DCC ID	ENCAB377OYK
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7112	7113

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RTCB	Product_ID: A305-078A Lot_ID: 1 Source: Bethyl Labs Target Name: RTCB-human

Experiment Status

	BGHcLV31-17	BGHcLV31-18
Sample_ID	BGHcLV31-17	BGHcLV31-18
Sample Name
Sample Name	RTCB-BGHcLV31-17	RTCB-BGHcLV31-18
RBP	RTCB	RTCB
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10295	10296

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-17	BGHcLV31-18
Sample #	9	10
Sample Name	RTCB-BGHcLV31-17	RTCB-BGHcLV31-18
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	287	286
Peak_Molarity	71.80	64.20
libSampleQC_DNA_Well	DNA_Library_set52/set1/A9.png	DNA_Library_set52/set1/B9.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set52/set1/A2.png	RNA_Library_set52/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-17	BGHcLV31-18
RBP	RTCB	RTCB
Batch_ID	BGHcLV31	BGHcLV31
WB_result	70.400	75.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3186	3187

Sequencing Information

	BGHcLV31-17	BGHcLV31-18
Sample_ID	BGHcLV31-17	BGHcLV31-18
Sample Name	RTCB-BGHcLV31-17	RTCB-BGHcLV31-18
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	330,654,516	70,349,368
total_aligned_reads	292,006,456	60,476,660
unique_aligned_reads	273,714,634	56,993,778
percent_uniqueAligned	0.82780	0.81015
correlation_replicates	0.998987	0.998987
spikein_reads	34,054	5,602
percent_spikeins	0.00010	0.00008
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1983	1984

Data Submission Information

	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-18	BGHcLV31-18	BGHcLV31-18	BGHcLV31-18
ENCODE_alias	brenton-graveley:RTCB-BGHcLV31	brenton-graveley:RTCB-BGHcLV31-17	brenton-graveley:L-RTCB-BGHcLV31-17	brenton-graveley:RTCB-BGHcLV31-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RTCB-BGHcLV31-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RTCB-BGHcLV31-HepG2	brenton-graveley:RTCB-BGHcLV31-18	brenton-graveley:L-RTCB-BGHcLV31-18	brenton-graveley:RTCB-BGHcLV31-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RTCB-BGHcLV31-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR726RTM	ENCBS550JRC	ENCLB182CTD	ENCFF774EFX	ENCFF084BEY	ENCSR143VRA	ENCBS156HXW	ENCLB126CBQ	ENCFF761WLR	ENCFF226PDQ
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	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-17	BGHcLV31-18	BGHcLV31-18	BGHcLV31-18	BGHcLV31-18
Sample Name	RTCB-BGHcLV31-17	RTCB-BGHcLV31-17	RTCB-BGHcLV31-17	RTCB-BGHcLV31-17	RTCB-BGHcLV31-17	RTCB-BGHcLV31-17	RTCB-BGHcLV31-18	RTCB-BGHcLV31-18	RTCB-BGHcLV31-18	RTCB-BGHcLV31-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RTCB-BGHcLV31-17.pdf	L-RTCB-BGHcLV31-17.pdf				RTCB-BGHcLV31-18.pdf	L-RTCB-BGHcLV31-18.pdf
ID	7448	7507	7615	7725	7835	7940	7508	7616	7726	7836

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
RTCB-BGHcLV31-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1983	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6529
RTCB-BGHcLV31-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1983	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6583
RTCB-BGHcLV31-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1983					GRCh38	V40	RTCB-BGHcLV31-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGHcLV31-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18450
RTCB-BGHcLV31-17_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1983					GRCh38	V40	RTCB-BGHcLV31-17/Aligned.sortedByCoord.out.bam		ENCORE2	18504
RTCB-BGHcLV31-17_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1983					GRCh38	V40	RTCB-BGHcLV31-17/Aligned.sortedByCoord.out.bam		ENCORE2	18558
RTCB-BGHcLV31-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1983					GRCh38	V40	RTCB-BGHcLV31-17/Aligned.sortedByCoord.out.bam		ENCORE2	18612
RTCB-BGHcLV31-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1983					GRCh38	V40	RTCB-BGHcLV31-17/Aligned.sortedByCoord.out.bam		ENCORE2	18666
RTCB-BGHcLV31-17_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1983					GRCh38	V40	RTCB-BGHcLV31-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGHcLV31-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18720
RTCB-BGHcLV31-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1984	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6530
RTCB-BGHcLV31-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1984	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6584
RTCB-BGHcLV31-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1984					GRCh38	V40	RTCB-BGHcLV31-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGHcLV31-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18451
RTCB-BGHcLV31-18_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1984					GRCh38	V40	RTCB-BGHcLV31-18/Aligned.sortedByCoord.out.bam		ENCORE2	18505
RTCB-BGHcLV31-18_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1984					GRCh38	V40	RTCB-BGHcLV31-18/Aligned.sortedByCoord.out.bam		ENCORE2	18559
RTCB-BGHcLV31-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1984					GRCh38	V40	RTCB-BGHcLV31-18/Aligned.sortedByCoord.out.bam		ENCORE2	18613
RTCB-BGHcLV31-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1984					GRCh38	V40	RTCB-BGHcLV31-18/Aligned.sortedByCoord.out.bam		ENCORE2	18667
RTCB-BGHcLV31-18_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1984					GRCh38	V40	RTCB-BGHcLV31-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGHcLV31-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18721