ROCK2 RNA-Seq in K562

General Information


RBP	ROCK2
Cell_Line	K562
Method	CRISPR
Exp_Name	ROCK2-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ROCK2-BGKcLV35-35
Rep2	ROCK2-BGKcLV35-36
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	51.2
Rep2_qPCR	59.2
Rep1_WB	70.3
Rep2_WB	70.7402
Antibody Cat#	A300-047A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB201RXT
Status	Submitted
Project	ENCORE2
ID	958

Experiment Information (Status: Submitting)

	BGKcLV35-35	BGKcLV35-36
idx	1312	1313
TRCN#_or_BGC#	BGC#0000791	BGC#0000791
shRNA_or_gRNA_sequence	TGTTTAGGGAGGTACGACTT	TGTTTAGGGAGGTACGACTT
PAM	GGG	GGG
Name	ROCK2_94	ROCK2_94
Sample_ID	BGKcLV35-35	BGKcLV35-36
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	ROCK2	ROCK2
qPCR_result	51.2	59.2
Ave_qPCR	55.2
RT-qPCR_primer-F	tgacccagcagatgatcaag
RT-qPCR_primer-R	cgaatctggctctcttcagc
protein_conc	3839	3466
WB_result	70.3	70.7402
Ave_WB	70.5
WB_DONE_date	6/14/22
MW	161KD
IP
antibody_Cat#	A300-047A	LOT #1
Antibody DCC ID	ENCAB201RXT
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5458	5459

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

	BGKcLV35-35	BGKcLV35-36
Sample_ID	BGKcLV35-35	BGKcLV35-36
Sample Name
Sample Name	ROCK2-BGKcLV35-35	ROCK2-BGKcLV35-36
RBP	ROCK2	ROCK2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10873	10874

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-35	BGKcLV35-36
Sample #	39	40
Sample Name	ROCK2-BGKcLV35-35	ROCK2-BGKcLV35-36
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	278	278
Peak_Molarity	43.00	21.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/G9.png	DNA_Library_set54-56/set3/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/G5.png	RNA_Library_set54-56/set2/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-35	BGKcLV35-36
RBP	ROCK2	ROCK2
Batch_ID	BGKcLV35	BGKcLV35
WB_result	70.300	70.740
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3356	3357

Sequencing Information

	BGKcLV35-35	BGKcLV35-36
Sample_ID	BGKcLV35-35	BGKcLV35-36
Sample Name	ROCK2-BGKcLV35-35	ROCK2-BGKcLV35-36
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	59,828,050	62,229,944
total_aligned_reads	53,853,870	53,337,688
unique_aligned_reads	49,386,416	48,990,492
percent_uniqueAligned	0.82547	0.78725
correlation_replicates	0.986897	0.986897
spikein_reads	7,520	9,446
percent_spikeins	0.00013	0.00015
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2235	2236

Data Submission Information DCC submission information was not avaliable

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-BGKcLV35-35_S41_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2235	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8510
ROCK2-BGKcLV35-35_S41_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2235	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8560
ROCK2-BGKcLV35-35_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2235					GRCh38	V40	ROCK2-BGKcLV35-35/Aligned.sortedByCoord.out.bam		ENCORE2	17756
ROCK2-BGKcLV35-35_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2235					GRCh38	V40	ROCK2-BGKcLV35-35/Aligned.sortedByCoord.out.bam		ENCORE2	17806
ROCK2-BGKcLV35-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2235					GRCh38	V40	ROCK2-BGKcLV35-35/Aligned.sortedByCoord.out.bam		ENCORE2	17856
ROCK2-BGKcLV35-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2235					GRCh38	V40	ROCK2-BGKcLV35-35/Aligned.sortedByCoord.out.bam		ENCORE2	17906
ROCK2-BGKcLV35-35_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2235					GRCh38	V40	ROCK2-BGKcLV35-35_S41_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGKcLV35-35_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17956
ROCK2-BGKcLV35-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2235					GRCh38	V40	ROCK2-BGKcLV35-35_S41_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGKcLV35-35_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29297
ROCK2-BGKcLV35-36_S42_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2236	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8511
ROCK2-BGKcLV35-36_S42_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2236	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8561
ROCK2-BGKcLV35-36_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2236					GRCh38	V40	ROCK2-BGKcLV35-36/Aligned.sortedByCoord.out.bam		ENCORE2	17757
ROCK2-BGKcLV35-36_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2236					GRCh38	V40	ROCK2-BGKcLV35-36/Aligned.sortedByCoord.out.bam		ENCORE2	17807
ROCK2-BGKcLV35-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2236					GRCh38	V40	ROCK2-BGKcLV35-36/Aligned.sortedByCoord.out.bam		ENCORE2	17857
ROCK2-BGKcLV35-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2236					GRCh38	V40	ROCK2-BGKcLV35-36/Aligned.sortedByCoord.out.bam		ENCORE2	17907
ROCK2-BGKcLV35-36_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2236					GRCh38	V40	ROCK2-BGKcLV35-36_S42_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGKcLV35-36_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17957
ROCK2-BGKcLV35-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2236					GRCh38	V40	ROCK2-BGKcLV35-36_S42_R1_001.filtered.trimmed.paired.fastq.gz,ROCK2-BGKcLV35-36_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29298