SMAD5 RNA-Seq in K562

General Information


RBP	SMAD5
Cell_Line	K562
Method	CRISPR
Exp_Name	SMAD5-BGKcLV19-K562
ENCODE_series_ID	ENCSR747UUF
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR649MBU
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	SMAD5-BGKcLV19-47
Rep2	SMAD5-BGKcLV19-48
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	90.8
Rep2_WB	94.7
Antibody Cat#	39-5700
Antibody Lot#	LOT# SA247535
Antibody DCC ID	ENCAB746HXR
Status	Released
Project	ENCODE4
ID	59

Experiment Information (Status: Released)

	BGKcLV19-47	BGKcLV19-48
idx	721	722
TRCN#_or_BGC#	BGC#0000409	BGC#0000409
shRNA_or_gRNA_sequence	TCATCATGAGCTAAAGCCGT	TCATCATGAGCTAAAGCCGT
PAM	TGG	TGG
Name	SMAD5_93	SMAD5_93
Sample_ID	BGKcLV19-47	BGKcLV19-48
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	SMAD5	SMAD5
qPCR_result	0	0
Ave_qPCR	0.0
RT-qPCR_primer-F	GAGTTTGCTCAGCTTCTGGC
RT-qPCR_primer-R	CTGCCGGTGATATTCTGCTC
protein_conc	4287	3256
WB_result	90.8	94.7
Ave_WB	92.7
WB_DONE_date	11/14/19	jess
MW	52KD
IP	Mouse / Ig
antibody_Cat#	39-5700	LOT# SA247535
Antibody DCC ID	ENCAB746HXR
submitted_to_DCC_date	11/16/20
Rep1_TPM	15.8	0
Rep2_TPM	14.2	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4841	4842

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMAD5	Product_ID: 39-5700 Lot_ID: SA247535 Source: Thermo Fisher Target Name: SMAD5-human

Experiment Status

	BGKcLV19-47	BGKcLV19-48
Sample_ID	BGKcLV19-47	BGKcLV19-48
Sample Name
Sample Name	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-48
RBP	SMAD5	SMAD5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5711	5712

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-47	BGKcLV19-48
Sample #	25	26
Sample Name	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-48
Sample_Name_Alias
Index Well Position	C03	D03
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	309	309
Peak_Molarity	164.00	97.80
libSampleQC_DNA_Well	DNA_Library_set45/set1/C3.png	DNA_Library_set45/set1/D3.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set45/set1/C3.png	RNA_Library_set45/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-47	BGKcLV19-48
RBP	SMAD5	SMAD5
Batch_ID	BGKcLV19	BGKcLV19
WB_result	90.800	94.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	799	800

Sequencing Information

	BGKcLV19-47	BGKcLV19-48
Sample_ID	BGKcLV19-47	BGKcLV19-48
Sample Name	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-48
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	208,242,428	133,922,522
total_aligned_reads	197,980,228	124,625,196
unique_aligned_reads	180,842,084	113,907,236
percent_uniqueAligned	0.86842	0.85055
correlation_replicates	0.989573	0.989573
spikein_reads	179,450	67,962
percent_spikeins	0.00086	0.00051
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	430	431

Data Submission Information

	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-48	BGKcLV19-48	BGKcLV19-48	BGKcLV19-48
ENCODE_alias	brenton-graveley:SMAD5-BGKcLV19	brenton-graveley:SMAD5-BGKcLV19-47	brenton-graveley:L-SMAD5-BGKcLV19-47	brenton-graveley:SMAD5-BGKcLV19-47_S19_R1_001.fastq.gz	brenton-graveley:SMAD5-BGKcLV19-47_S19_R2_001.fastq.gz	brenton-graveley:SMAD5-BGKcLV19-K562	brenton-graveley:SMAD5-BGKcLV19-48	brenton-graveley:L-SMAD5-BGKcLV19-48	brenton-graveley:SMAD5-BGKcLV19-48_S20_R1_001.fastq.gz	brenton-graveley:SMAD5-BGKcLV19-48_S20_R2_001.fastq.gz
ENCODE_accession	ENCSR649MBU	ENCBS190TOX	ENCLB219FBY	ENCFF182QWR	ENCFF555MDU	ENCSR747UUF	ENCBS273YVK	ENCLB677HEM	ENCFF004ROJ	ENCFF251FKD
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	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-47	BGKcLV19-48	BGKcLV19-48	BGKcLV19-48	BGKcLV19-48
Sample Name	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-47	SMAD5-BGKcLV19-48	SMAD5-BGKcLV19-48	SMAD5-BGKcLV19-48	SMAD5-BGKcLV19-48
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		SMAD5-BGKcLV19-47.pdf	L-SMAD5-BGKcLV19-47.pdf				SMAD5-BGKcLV19-48.pdf	L-SMAD5-BGKcLV19-48.pdf
ID	2099	2153	2223	2293	2363	7330	2154	2224	2294	2364

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
SMAD5-BGKcLV19-47_S19_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	430	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1252
SMAD5-BGKcLV19-47_S19_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	430	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1302
SMAD5-BGKcLV19-47_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	430					GRCh38	V40	SMAD5-BGKcLV19-47_S19_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGKcLV19-47_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25245
SMAD5-BGKcLV19-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	430					GRCh38	V40	SMAD5-BGKcLV19-47_S19_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGKcLV19-47_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27199
SMAD5-BGKcLV19-47_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	430					GRCh38	V40	SMAD5-BGKcLV19-47/Aligned.sortedByCoord.out.bam		ENCORE2	27249
SMAD5-BGKcLV19-47_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	430					GRCh38	V40	SMAD5-BGKcLV19-47/Aligned.sortedByCoord.out.bam		ENCORE2	27299
SMAD5-BGKcLV19-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	430					GRCh38	V40	SMAD5-BGKcLV19-47/Aligned.sortedByCoord.out.bam		ENCORE2	27349
SMAD5-BGKcLV19-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	430					GRCh38	V40	SMAD5-BGKcLV19-47/Aligned.sortedByCoord.out.bam		ENCORE2	27399
SMAD5-BGKcLV19-48_S20_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	431	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1253
SMAD5-BGKcLV19-48_S20_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	431	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1303
SMAD5-BGKcLV19-48_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	431					GRCh38	V40	SMAD5-BGKcLV19-48_S20_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGKcLV19-48_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25246
SMAD5-BGKcLV19-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	431					GRCh38	V40	SMAD5-BGKcLV19-48_S20_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGKcLV19-48_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27200
SMAD5-BGKcLV19-48_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	431					GRCh38	V40	SMAD5-BGKcLV19-48/Aligned.sortedByCoord.out.bam		ENCORE2	27250
SMAD5-BGKcLV19-48_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	431					GRCh38	V40	SMAD5-BGKcLV19-48/Aligned.sortedByCoord.out.bam		ENCORE2	27300
SMAD5-BGKcLV19-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	431					GRCh38	V40	SMAD5-BGKcLV19-48/Aligned.sortedByCoord.out.bam		ENCORE2	27350
SMAD5-BGKcLV19-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	431					GRCh38	V40	SMAD5-BGKcLV19-48/Aligned.sortedByCoord.out.bam		ENCORE2	27400