ROCK2 RNA-Seq in HepG2

General Information


RBP	ROCK2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ROCK2-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR417QKN
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR034VEC
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	ROCK2-BGHcLV32-41
Rep2	ROCK2-BGHcLV32-42
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	44.3
Rep2_qPCR	61.2
Rep1_WB	72.7
Rep2_WB	84.1
Antibody Cat#	A300-047A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB201RXT
Status	Submitted
Project	ENCODE4
ID	936

Experiment Information (Status: Released)

	BGHcLV32-41	BGHcLV32-42
idx	1042	1043
TRCN#_or_BGC#	BGC#0000791	BGC#0000791
shRNA_or_gRNA_sequence	TGTTTAGGGAGGTACGACTT	TGTTTAGGGAGGTACGACTT
PAM	GGG	GGG
Name	ROCK2_94	ROCK2_94
Sample_ID	BGHcLV32-41	BGHcLV32-42
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	ROCK2	ROCK2
qPCR_result	44.3	61.2
Ave_qPCR	52.8
RT-qPCR_primer-F	tgacccagcagatgatcaag
RT-qPCR_primer-R	cgaatctggctctcttcagc
protein_conc	5503	4488
WB_result	72.7	84.1
Ave_WB	78.4
WB_DONE_date	3/16/22
MW	161KD
IP
antibody_Cat#	A300-047A	LOT #1
Antibody DCC ID	ENCAB201RXT	8/4/22
submitted_to_DCC_date
Rep1_TPM	8	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	9269	9270

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ROCK2	Product_ID: A300-047A Lot_ID: 1 Source: Bethyl Labs Target Name: ROCK2-human

Experiment Status

	BGHcLV32-41	BGHcLV32-42
Sample_ID	BGHcLV32-41	BGHcLV32-42
Sample Name
Sample Name	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-42
RBP	ROCK2	ROCK2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10371	10372

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-41	BGHcLV32-42
Sample #	45	46
Sample Name	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-42
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	300	297
Peak_Molarity	59.60	70.90
libSampleQC_DNA_Well	DNA_Library_set52/set2/E6.png	DNA_Library_set52/set2/F6.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set52/set2/A9.png	RNA_Library_set52/set2/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-41	BGHcLV32-42
RBP	ROCK2	ROCK2
Batch_ID	BGHcLV32	BGHcLV32
WB_result	52.000	75.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3222	3223

Sequencing Information

	BGHcLV32-41	BGHcLV32-42
Sample_ID	BGHcLV32-41	BGHcLV32-42
Sample Name	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-42
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	85,023,656	64,926,252
total_aligned_reads	66,463,116	51,312,216
unique_aligned_reads	62,399,560	48,343,020
percent_uniqueAligned	0.73391	0.74458
correlation_replicates	0.998352	0.998352
spikein_reads	7,180	4,828
percent_spikeins	0.00008	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2017	2018

Data Submission Information

	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-42	BGHcLV32-42	BGHcLV32-42	BGHcLV32-42
ENCODE_alias	brenton-graveley:ROCK2-BGHcLV32	brenton-graveley:ROCK2-BGHcLV32-41	brenton-graveley:L-ROCK2-BGHcLV32-41	brenton-graveley:ROCK2-BGHcLV32-41_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ROCK2-BGHcLV32-41_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ROCK2-BGHcLV32-HepG2	brenton-graveley:ROCK2-BGHcLV32-42	brenton-graveley:L-ROCK2-BGHcLV32-42	brenton-graveley:ROCK2-BGHcLV32-42_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ROCK2-BGHcLV32-42_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR034VEC	ENCBS712HXB	ENCLB934XDP	ENCFF877QZL	ENCFF639EZB	ENCSR417QKN	ENCBS925GYT	ENCLB354VMJ	ENCFF013UMZ	ENCFF809PBA
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	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-41	BGHcLV32-42	BGHcLV32-42	BGHcLV32-42	BGHcLV32-42
Sample Name	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-41	ROCK2-BGHcLV32-42	ROCK2-BGHcLV32-42	ROCK2-BGHcLV32-42	ROCK2-BGHcLV32-42
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		ROCK2-BGHcLV32-41.pdf	L-ROCK2-BGHcLV32-41.pdf				ROCK2-BGHcLV32-42.pdf	L-ROCK2-BGHcLV32-42.pdf
ID	7466	7539	7651	7759	7869	7956	7540	7652	7760	7870

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
ROCK2-BGHcLV32-41_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2017	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6517
ROCK2-BGHcLV32-41_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2017	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6571
ROCK2-BGHcLV32-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2017					GRCh38	V40	ROCK2-BGHcLV32-41_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGHcLV32-41_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18438
ROCK2-BGHcLV32-41_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	2017					GRCh38	V40	ROCK2-BGHcLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	18492
ROCK2-BGHcLV32-41_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	2017					GRCh38	V40	ROCK2-BGHcLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	18546
ROCK2-BGHcLV32-41_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	2017					GRCh38	V40	ROCK2-BGHcLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	18600
ROCK2-BGHcLV32-41_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	2017					GRCh38	V40	ROCK2-BGHcLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	18654
ROCK2-BGHcLV32-41_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2017					GRCh38	V40	ROCK2-BGHcLV32-41_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGHcLV32-41_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18708
ROCK2-BGHcLV32-42_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2018	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6518
ROCK2-BGHcLV32-42_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2018	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6572
ROCK2-BGHcLV32-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2018					GRCh38	V40	ROCK2-BGHcLV32-42_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGHcLV32-42_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18439
ROCK2-BGHcLV32-42_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	2018					GRCh38	V40	ROCK2-BGHcLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	18493
ROCK2-BGHcLV32-42_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	2018					GRCh38	V40	ROCK2-BGHcLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	18547
ROCK2-BGHcLV32-42_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	2018					GRCh38	V40	ROCK2-BGHcLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	18601
ROCK2-BGHcLV32-42_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	2018					GRCh38	V40	ROCK2-BGHcLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	18655
ROCK2-BGHcLV32-42_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2018					GRCh38	V40	ROCK2-BGHcLV32-42_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGHcLV32-42_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18709