CARHSP1 RNA-Seq in K562

General Information


RBP	CARHSP1
Cell_Line	K562
Method	CRISPR
Exp_Name	CARHSP1-BGKcLV26-K562
ENCODE_series_ID	ENCSR100DTM
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR876IJP
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CARHSP1-BGKcLV26-55
Rep2	CARHSP1-BGKcLV26-56
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	20.6
Rep2_qPCR	31.5
Rep1_WB	57.0
Rep2_WB	56.6
Antibody Cat#	A303-908A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB401VFW
Status	Released
Project	ENCODE4
ID	801

Experiment Information (Status: Released)

	BGKcLV26-55	BGKcLV26-56
idx	918	919
TRCN#_or_BGC#	BGC#0000664	BGC#0000664
shRNA_or_gRNA_sequence	ACGCCGAGAAGGTCCTCGTC	ACGCCGAGAAGGTCCTCGTC
PAM	CGG	CGG
Name	CARHSP1_96	CARHSP1_96
Sample_ID	BGKcLV26-55	BGKcLV26-56
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	CARHSP1	CARHSP1
qPCR_result	20.6	31.5
Ave_qPCR	26.0
RT-qPCR_primer-F	tgtggaaggggagtatgtcc
RT-qPCR_primer-R	gcctgcagcttctcattctt
protein_conc	5079	5077
WB_result	57.0	56.6
Ave_WB	56.8
WB_DONE_date	5/10/21	jess
MW	16kda
IP	Rabbit / I
antibody_Cat#	A303-908A	LOT# 1
Antibody DCC ID	ENCAB401VFW	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5050	5051

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CARHSP1	Product_ID: A303-908A Lot_ID: 1 Source: Bethyl Labs Target Name: CARHSP1-human

Experiment Status

	BGKcLV26-55	BGKcLV26-56
Sample_ID	BGKcLV26-55	BGKcLV26-56
Sample Name
Sample Name	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-56
RBP	CARHSP1	CARHSP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9783	9784

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-55	BGKcLV26-56
Sample #	41	42
Sample Name	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-56
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	291	300
Peak_Molarity	123.00	99.20
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/A6.png	DNA_Library_set48-49/set1/B6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set48-49/set1/A6.png	RNA_Library_set48-49/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-55	BGKcLV26-56
RBP	CARHSP1	CARHSP1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	57.000	56.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1600	1601

Sequencing Information

	BGKcLV26-55	BGKcLV26-56
Sample_ID	BGKcLV26-55	BGKcLV26-56
Sample Name	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-56
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	77,868,310	77,616,994
total_aligned_reads	71,089,060	67,338,650
unique_aligned_reads	65,234,176	61,669,728
percent_uniqueAligned	0.83775	0.79454
correlation_replicates	0.998561	0.998561
spikein_reads	39,464	19,110
percent_spikeins	0.00051	0.00025
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1777	1778

Data Submission Information

	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-56	BGKcLV26-56	BGKcLV26-56	BGKcLV26-56
ENCODE_alias	brenton-graveley:CARHSP1-BGKcLV26	brenton-graveley:CARHSP1-BGKcLV26-55	brenton-graveley:L-CARHSP1-BGKcLV26-55	brenton-graveley:CARHSP1-BGKcLV26-55_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARHSP1-BGKcLV26-55_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARHSP1-BGKcLV26-K562	brenton-graveley:CARHSP1-BGKcLV26-56	brenton-graveley:L-CARHSP1-BGKcLV26-56	brenton-graveley:CARHSP1-BGKcLV26-56_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARHSP1-BGKcLV26-56_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR876IJP	ENCBS430ULM	ENCLB305TDC	ENCFF957EEM	ENCFF975VMW	ENCSR100DTM	ENCBS561VWT	ENCLB111UPD	ENCFF018DHS	ENCFF880TMB
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	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-55	BGKcLV26-56	BGKcLV26-56	BGKcLV26-56	BGKcLV26-56
Sample Name	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-55	CARHSP1-BGKcLV26-56	CARHSP1-BGKcLV26-56	CARHSP1-BGKcLV26-56	CARHSP1-BGKcLV26-56
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		CARHSP1-BGKcLV26-55.pdf	L-CARHSP1-BGKcLV26-55.pdf				CARHSP1-BGKcLV26-56.pdf	L-CARHSP1-BGKcLV26-56.pdf
ID	3466	3566	3700	3834	3968	7114	3567	3701	3835	3969

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
CARHSP1-BGKcLV26-55_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1777	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3870
CARHSP1-BGKcLV26-55_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1777	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3920
CARHSP1-BGKcLV26-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1777					GRCh38	V40	CARHSP1-BGKcLV26-55_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGKcLV26-55_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25557
CARHSP1-BGKcLV26-55_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1777					GRCh38	V40	CARHSP1-BGKcLV26-55_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGKcLV26-55_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25607
CARHSP1-BGKcLV26-55_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1777					GRCh38	V40	CARHSP1-BGKcLV26-55/Aligned.sortedByCoord.out.bam		ENCORE2	26573
CARHSP1-BGKcLV26-55_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1777					GRCh38	V40	CARHSP1-BGKcLV26-55/Aligned.sortedByCoord.out.bam		ENCORE2	26623
CARHSP1-BGKcLV26-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1777					GRCh38	V40	CARHSP1-BGKcLV26-55/Aligned.sortedByCoord.out.bam		ENCORE2	26673
CARHSP1-BGKcLV26-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1777					GRCh38	V40	CARHSP1-BGKcLV26-55/Aligned.sortedByCoord.out.bam		ENCORE2	26723
CARHSP1-BGKcLV26-56_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1778	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3871
CARHSP1-BGKcLV26-56_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1778	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3921
CARHSP1-BGKcLV26-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1778					GRCh38	V40	CARHSP1-BGKcLV26-56_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGKcLV26-56_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25558
CARHSP1-BGKcLV26-56_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1778					GRCh38	V40	CARHSP1-BGKcLV26-56_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGKcLV26-56_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25608
CARHSP1-BGKcLV26-56_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1778					GRCh38	V40	CARHSP1-BGKcLV26-56/Aligned.sortedByCoord.out.bam		ENCORE2	26574
CARHSP1-BGKcLV26-56_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1778					GRCh38	V40	CARHSP1-BGKcLV26-56/Aligned.sortedByCoord.out.bam		ENCORE2	26624
CARHSP1-BGKcLV26-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1778					GRCh38	V40	CARHSP1-BGKcLV26-56/Aligned.sortedByCoord.out.bam		ENCORE2	26674
CARHSP1-BGKcLV26-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1778					GRCh38	V40	CARHSP1-BGKcLV26-56/Aligned.sortedByCoord.out.bam		ENCORE2	26724