CIRBP RNA-Seq in K562

General Information


RBP	CIRBP
Cell_Line	K562
Method	CRISPR
Exp_Name	CIRBP-BGKcLV11-K562
ENCODE_series_ID	ENCSR158LDQ
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR452KAP
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	CIRBP-BGKcLV11-33
Rep2	CIRBP-BGKcLV11-34
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	41.4
Rep2_qPCR	47.4
Rep1_WB	73.5
Rep2_WB	80.7
Antibody Cat#	RN032P
Antibody Lot#
Antibody DCC ID	ENCAB000BFF
Status	Released
Project	ENCODE4
ID	166

Experiment Information (Status: Released)

	BGKcLV11-33	BGKcLV11-34
idx	349	350
TRCN#_or_BGC#	BGC#0000253	BGC#0000253
shRNA_or_gRNA_sequence	TGAGAACATTGACGACGCTA	TGAGAACATTGACGACGCTA
PAM	AGG	AGG
Name	CIRBP_95	CIRBP_95
Sample_ID	BGKcLV11-33	BGKcLV11-34
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	CIRBP	CIRBP
qPCR_result	41.4	47.4
Ave_qPCR	44.4
RT-qPCR_primer-F	TGTGGTGCGCTGTCTTCC
RT-qPCR_primer-R	AAACTCAGCCCTCCAACAAA
protein_conc	3472	2949
WB_result	73.5	80.7
Ave_WB	77.1	NEED DISCUSSion
WB_DONE_date	1/31/19
MW	19 kDa
IP
antibody_Cat#	RN032P
Antibody DCC ID	ENCAB000BFF
submitted_to_DCC_date	2/22/19
Rep1_TPM	169.5	0
Rep2_TPM	101.5	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4449	4450

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CIRBP	Product_ID: RN032P Lot_ID: 1 Source: MBLI Target Name: CIRBP-human

Experiment Status

	BGKcLV11-33	BGKcLV11-34
Sample_ID	BGKcLV11-33	BGKcLV11-34
Sample Name	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-34
Sample Name	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-34
RBP	CIRBP	CIRBP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2677	2678

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-33	BGKcLV11-34
Sample #	5	6
Sample Name	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-34
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-E1	1-F1
Tecan	38.25	37.67
Tecan_date	2019-03-13	2019-03-13
Size_bp	299	287
Peak_Molarity	50.10	25.60
libSampleQC_DNA_Well	DNA_Library_set42/set1/E1.png	DNA_Library_set42/set1/F1.png
RIN	8.3	8.3
libSample_RNA_Well	RNA_Library_set42/set1/E1.png	RNA_Library_set42/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-33	BGKcLV11-34
RBP	CIRBP	CIRBP
Batch_ID	BGKcLV11	BGKcLV11
WB_result	73.500	80.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	5	6

Sequencing Information

	BGKcLV11-33	BGKcLV11-34
Sample_ID	BGKcLV11-33	BGKcLV11-34
Sample Name	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-34
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	45,735,636	79,113,196
total_aligned_reads	43,619,198	75,740,758
unique_aligned_reads	39,475,606	67,651,940
percent_uniqueAligned	0.86313	0.85513
correlation_replicates	0.998607	0.998607
spikein_reads	64,504	88,338
percent_spikeins	0.00141	0.00112
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	11	12

Data Submission Information

	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-34	BGKcLV11-34	BGKcLV11-34	BGKcLV11-34
ENCODE_alias	brenton-graveley:CIRBP-BGKcLV11	brenton-graveley:CIRBP-BGKcLV11-33	brenton-graveley:L-CIRBP-BGKcLV11-33	brenton-graveley:CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CIRBP-BGKcLV11-K562	brenton-graveley:CIRBP-BGKcLV11-34	brenton-graveley:L-CIRBP-BGKcLV11-34	brenton-graveley:CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR452KAP	ENCBS593KZI	ENCLB167UXJ	ENCFF466ADQ	ENCFF003PXR	ENCSR158LDQ	ENCBS720APO	ENCLB955YSA	ENCFF892IAG	ENCFF153TJA
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	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-33	BGKcLV11-34	BGKcLV11-34	BGKcLV11-34	BGKcLV11-34
Sample Name	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-33	CIRBP-BGKcLV11-34	CIRBP-BGKcLV11-34	CIRBP-BGKcLV11-34	CIRBP-BGKcLV11-34
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		CIRBP-BGKcLV11-33.pdf	L-CIRBP-BGKcLV11-33.pdf				CIRBP-BGKcLV11-34.pdf	L-CIRBP-BGKcLV11-34.pdf
ID	762	819	901	961	1043	7139	820	902	962	1044

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
CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	11	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	343
CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	11	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	425
CIRBP-BGKcLV11-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	11					GRCh38	V40	CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23682
CIRBP-BGKcLV11-33_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	11					GRCh38	V40	CIRBP-BGKcLV11-33/Aligned.sortedByCoord.out.bam		ENCORE2	23764
CIRBP-BGKcLV11-33_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	11					GRCh38	V40	CIRBP-BGKcLV11-33/Aligned.sortedByCoord.out.bam		ENCORE2	23846
CIRBP-BGKcLV11-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	11					GRCh38	V40	CIRBP-BGKcLV11-33/Aligned.sortedByCoord.out.bam		ENCORE2	23928
CIRBP-BGKcLV11-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	11					GRCh38	V40	CIRBP-BGKcLV11-33/Aligned.sortedByCoord.out.bam		ENCORE2	24010
CIRBP-BGKcLV11-33_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	11					GRCh38	V40	CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGKcLV11-33_ATCCACTG+AGGTGCGT_HK3H2DSXX_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24092
CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	12	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	344
CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	12	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	426
CIRBP-BGKcLV11-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	12					GRCh38	V40	CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23683
CIRBP-BGKcLV11-34_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	12					GRCh38	V40	CIRBP-BGKcLV11-34/Aligned.sortedByCoord.out.bam		ENCORE2	23765
CIRBP-BGKcLV11-34_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	12					GRCh38	V40	CIRBP-BGKcLV11-34/Aligned.sortedByCoord.out.bam		ENCORE2	23847
CIRBP-BGKcLV11-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	12					GRCh38	V40	CIRBP-BGKcLV11-34/Aligned.sortedByCoord.out.bam		ENCORE2	23929
CIRBP-BGKcLV11-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	12					GRCh38	V40	CIRBP-BGKcLV11-34/Aligned.sortedByCoord.out.bam		ENCORE2	24011
CIRBP-BGKcLV11-34_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	12					GRCh38	V40	CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGKcLV11-34_GCTTGTCA+GAACATAC_HK3H2DSXX_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24093