RBM19 RNA-Seq in HepG2

General Information


RBP	RBM19
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM19-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR043MAQ
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR532IHF
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	RBM19-BGHcLV20-25
Rep2	RBM19-BGHcLV20-26
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	2.0
Rep2_qPCR	0.0
Rep1_WB	96.6
Rep2_WB	98.6
Antibody Cat#	PA5-58567
Antibody Lot#	LOT# UC2743817
Antibody DCC ID	ENCAB385QQI
Status	Released
Project	ENCODE4
ID	77

Experiment Information (Status: Released)

	BGHcLV20-25	BGHcLV20-26
idx	575	576
TRCN#_or_BGC#	BGC#0000484	BGC#0000484
shRNA_or_gRNA_sequence	CAGGCCATCATTCGCCCAAG	CAGGCCATCATTCGCCCAAG
PAM	TGG	TGG
Name	RBM19_94	RBM19_94
Sample_ID	BGHcLV20-25	BGHcLV20-26
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	RBM19	RBM19
qPCR_result	2.0	0.0
Ave_qPCR	1.0
RT-qPCR_primer-F	TGAACTTCGACTCCGATTCTG
RT-qPCR_primer-R	CATGTCCGACAGCTCCTTCT
protein_conc	5005	4161
WB_result	96.6	98.6
Ave_WB	97.6
WB_DONE_date	1/28/21	JESS
MW	107.3kDa
IP	Rabbit / I
antibody_Cat#	PA5-58567	LOT# UC2743817
Antibody DCC ID	ENCAB385QQI
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6730	6731

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM19	Product_ID: PA5-58567 Lot_ID: UC2743817 Source: Thermo Fisher Target Name: RBM19-human

Experiment Status

	BGHcLV20-25	BGHcLV20-26
Sample_ID	BGHcLV20-25	BGHcLV20-26
Sample Name
Sample Name	RBM19-BGHcLV20-25	RBM19-BGHcLV20-26
RBP	RBM19	RBM19
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5815	5816

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-25	BGHcLV20-26
Sample #	65	66
Sample Name	RBM19-BGHcLV20-25	RBM19-BGHcLV20-26
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	307	306
Peak_Molarity	114.00	83.20
libSampleQC_DNA_Well	DNA_Library_set45/set1/C8.png	DNA_Library_set45/set1/D8.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set45/set1/C8.png	RNA_Library_set45/set2/C11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-25	BGHcLV20-26
RBP	RBM19	RBM19
Batch_ID	BGHcLV20	BGHcLV20
WB_result	94.100	93.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	839	840

Sequencing Information

	BGHcLV20-25	BGHcLV20-26
Sample_ID	BGHcLV20-25	BGHcLV20-26
Sample Name	RBM19-BGHcLV20-25	RBM19-BGHcLV20-26
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	88,569,098	95,829,036
total_aligned_reads	85,926,194	88,424,796
unique_aligned_reads	81,141,476	83,292,808
percent_uniqueAligned	0.91614	0.86918
correlation_replicates	0.991472	0.991472
spikein_reads	55,706	43,504
percent_spikeins	0.00063	0.00045
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	470	471

Data Submission Information

	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-26	BGHcLV20-26	BGHcLV20-26	BGHcLV20-26
ENCODE_alias	brenton-graveley:RBM19-BGHcLV20	brenton-graveley:RBM19-BGHcLV20-25	brenton-graveley:L-RBM19-BGHcLV20-25	brenton-graveley:RBM19-BGHcLV20-25_S59_R1_001.fastq.gz	brenton-graveley:RBM19-BGHcLV20-25_S59_R2_001.fastq.gz	brenton-graveley:RBM19-BGHcLV20-HepG2	brenton-graveley:RBM19-BGHcLV20-26	brenton-graveley:L-RBM19-BGHcLV20-26	brenton-graveley:RBM19-BGHcLV20-26_S60_R1_001.fastq.gz	brenton-graveley:RBM19-BGHcLV20-26_S60_R2_001.fastq.gz
ENCODE_accession	ENCSR532IHF	ENCBS965FCH	ENCLB201RRL	ENCFF641TMF	ENCFF678ICT	ENCSR043MAQ	ENCBS637PVZ	ENCLB603JLY	ENCFF540XEB	ENCFF351NTZ
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	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-25	BGHcLV20-26	BGHcLV20-26	BGHcLV20-26	BGHcLV20-26
Sample Name	RBM19-BGHcLV20-25	RBM19-BGHcLV20-25	RBM19-BGHcLV20-25	RBM19-BGHcLV20-25	RBM19-BGHcLV20-25	RBM19-BGHcLV20-25	RBM19-BGHcLV20-26	RBM19-BGHcLV20-26	RBM19-BGHcLV20-26	RBM19-BGHcLV20-26
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45H_biosample_protocol	LV45H_library_protocol				LV45H_biosample_protocol	LV45H_library_protocol
protocol_URL		RBM19-BGHcLV20-25.pdf	L-RBM19-BGHcLV20-25.pdf				RBM19-BGHcLV20-26.pdf	L-RBM19-BGHcLV20-26.pdf
ID	2084	2123	2193	2263	2333	7298	2124	2194	2264	2334

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
RBM19-BGHcLV20-25_S59_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	470	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1316
RBM19-BGHcLV20-25_S59_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	470	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1336
RBM19-BGHcLV20-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	470					GRCh38	V40	RBM19-BGHcLV20-25_S59_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGHcLV20-25_S59_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24857
RBM19-BGHcLV20-25_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	470					GRCh38	V40	RBM19-BGHcLV20-25_S59_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGHcLV20-25_S59_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24877
RBM19-BGHcLV20-25_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	470					GRCh38	V40	RBM19-BGHcLV20-25/Aligned.sortedByCoord.out.bam		ENCORE2	25927
RBM19-BGHcLV20-25_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	470					GRCh38	V40	RBM19-BGHcLV20-25/Aligned.sortedByCoord.out.bam		ENCORE2	25947
RBM19-BGHcLV20-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	470					GRCh38	V40	RBM19-BGHcLV20-25/Aligned.sortedByCoord.out.bam		ENCORE2	25967
RBM19-BGHcLV20-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	470					GRCh38	V40	RBM19-BGHcLV20-25/Aligned.sortedByCoord.out.bam		ENCORE2	25987
RBM19-BGHcLV20-26_S60_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	471	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1317
RBM19-BGHcLV20-26_S60_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	471	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1337
RBM19-BGHcLV20-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	471					GRCh38	V40	RBM19-BGHcLV20-26_S60_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGHcLV20-26_S60_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24858
RBM19-BGHcLV20-26_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	471					GRCh38	V40	RBM19-BGHcLV20-26_S60_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGHcLV20-26_S60_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24878
RBM19-BGHcLV20-26_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	471					GRCh38	V40	RBM19-BGHcLV20-26/Aligned.sortedByCoord.out.bam		ENCORE2	25928
RBM19-BGHcLV20-26_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	471					GRCh38	V40	RBM19-BGHcLV20-26/Aligned.sortedByCoord.out.bam		ENCORE2	25948
RBM19-BGHcLV20-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	471					GRCh38	V40	RBM19-BGHcLV20-26/Aligned.sortedByCoord.out.bam		ENCORE2	25968
RBM19-BGHcLV20-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	471					GRCh38	V40	RBM19-BGHcLV20-26/Aligned.sortedByCoord.out.bam		ENCORE2	25988