title: Rrm4-Gfp iCLIP2 replicate 4

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

library_source: other

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcodes.fasta (using sample barcodes: Rrm4-Gfp iCLIP2 replicate 1: NNNNNTGGTCANNNN, Rrm4-Gfp iCLIP2 replicate 2: NNNNNATTGGCNNNN, Rrm4-Gfp iCLIP2 replicate 3: NNNNNCGTGATNNNN, Rrm4-Gfp iCLIP2 replicate 4: NNNNNGCCTAANNNN, Rrm4-Gfp iCLIP2 replicate 5: NNNNNCTGATCNNNN)
Mapping: STAR (v2.7.3a) with non-default parameters: --genomeDir Ensembl_release51_Umaydis521_2.0 --sjdbGTFfile Ustilago_maydis.Umaydis521_2.0.51.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 4000000000
Removal of reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.9), Bedtools (v2.27.1): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.0.0) with non-default parameter: umi_tools dedup --method unique
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Processed reads from all five replicates were merged into a single dataset, and subjected to peak calling using PureCLIP (version 1.3.1) with default parameters.
The resulting crosslink sites were then used to define binding sites with the R/Bioconductor package BindingSiteFinder (version 1.7.9). Initially, a pre-filtering step was implemented to retain only the most significant sites. Specifically, crosslink sites ranked in the lowest 5% by PureCLIP score—a measure of binding affinity strength provided by PureCLIP—were excluded. To account for gene expression levels and to improve the binding site quality, crosslink sites with the lowest 10% PureCLIP score per gene were filtered out. For defining the binding sites, processed crosslink sites within a distance closer than 8-nt were merged, requiring at least 2 out of 9 sites to be covered by crosslink events. The centers of the binding sites were iteratively positioned at crosslink events with the highest PureCLIP score and extended by 4-nt on either side, resulting in binding sites with 9-nt width. Furthermore, binding sites were deemed reproducible if they harbored more crosslink events than the 5th percentile of the crosslink distribution across all binding sites, with at least 2 crosslink events per binding site, observed in four out of five biological replicates.
Umaydis521_2.0 (Ensembl release 51)
bigWig files show all detected crosslink events for Rrm4-GFP, separated by minus and plus strands.
The BED file specifies  the coordinates of all 39472 binding sites (9-nt width) for Rrm4

molecule: other

organism: Mycosarcoma maydis

source_name: hyphae

growth_protocol: The cultivation conditions for Ustilago maydis are detailed in Brachmann et al., Mol Genet Genomics, 2004 (DOI: 10.1007/s00438-004-1047-z). The starting cultures were grown in CM medium supplemented with glucose at 28°C.

extract_protocol:
For a complete iCLIP2 experiment 150 mL shifted culture (OD600 = 0.5) was used. The cells were UV treated (254 nm, 1x 200 mJ/cm2, Biolink UV-Crosslinker, Vilber-Lourmat) and harvested, and lysed as detailed described before (see „Bead mill tube“). The cryogenic cell powder was resuspended in 2 mL iCLIP Lysis buffer (50 mM Tris–HCl, pH 7.4; 100 mM NaCl; 1% IGEPAL CA-630; 0.1% SDS, 0.5% sodium deoxycholate, 2 M urea (Roth) - in addition freshly added 2× Complete protease inhibitor EDTA-free (Merck, 11873580001), 1 mM DTT, 1 mM PMSF (+ 5 µl SUPERase-In Thermo Fisher) per 50 mL culture. Afterwards, the homogenisate was spun at 4°C, 10 min, and 16,200 g. The supernatant was carried into a fresh, pre-cooled tube and spun again. The respective supernatants were pooled and afterward separated into three fresh tubes containing 20 µl pre-washed GFP-Trap beads (Chromotek; gtma-20). The IP was conducted for 1 h, at 4°C under rotating conditions. Afterward, the beads were pooled in a 2 ml reaction tube and washed four times with 1 mL high-salt buffer (50 mM Tris–HCl, pH 7.4, 1 M NaCl, 1 mM EDTA, 1% IGEPAL CA-630, 0.1% SDS, 0.5% sodium deoxycholate). The beads were then washed twice within 1x PNK buffer (20 mM Tris–HCl, pH 7.4, 10 mM Mg2Cl, 0.2% Tween-20). The beads were then transferred into a fresh 1.5 mL reaction tube and again washed three times with 1x PNK buffer. The rest of the iCLIP2 procedure was adopted from the original iCLIP2 protocol including oligonucleotides (Buchbender et al., 2020). Running and blotting were performed as described before during Western blot analysis. Afterward, the respective membrane was washed with ice-cold 1x PBS buffer and then covered in a fresh transparent plastic bag and exposed to BAS Storage Phosphor Screen (GE Healthcare) for approximately 1 h or overnight at - 20°C. The screen was visualized by a TyphoonTM laser scanner (Cytiva), according to manufacturer information. An optional RNase I (Life Technologies, AM2295) treatment was performed after the immunoprecipitation. Various dilutions (ranging from 1:50 to 1:1500) were prepared in 1x PNK buffer and added to the beads.  The beads were incubated for 3 min, 37°C at 1000 rpm, and subsequently, washed with cold High-salt buffer and handled on ice.
Following immunoprecipitation, the remainder of the iCLIP2 procedure, including the use of oligonucleotides, was adopted from the original iCLIP2 protocol (Buchbender et al., 2020). cDNA libraries were quality controlled using a TapeStation system  (D1000 Sensitivity Kit), and their exact concentration was measured with a Qubit High Sensitivity Kit. The respective libraries were then pooled with equal molarity as described by Buchbender et al. (2020). Sequencing was performed by NextSeq 500/550 Illumina.

treatment_protocol: Hyphal growth was induced by shifting the cells to Nitrate minimal medium supplement with 1% glucose at 28°C, 200 rpm for 6h post-induction.

tag: strain

value: hyphae

value: wildtype expressing the RBP Rrm4 with C-terminal GFP tag

value: switch from yeast to hyphal growth

tag: time

value: 6 hours post hyphal induction


title: IVF_Let7d_scRNA-seq_C1

status: Public on Jan 14 2025

type: SRA

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the mouse reference genome from Gencode (vM25) using STAR aligner and gene features were counted by using featureCountsv (2.0.3).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw reads for each sample.
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample.

molecule: total RNA

organism: Mus musculus

growth_protocol: MicroRNA microinjected zygotes were kept until 8-cell-stage and then disassociated for further sequencing.

extract_protocol:
Custom-made Smart-seq2 protocol was implemented as before.
RNA libraries for scRNA-seq were prepared using Dual-indexed Illumina Nextera XT sequencing librarie kit.

treatment_protocol: Zygote were microinjected with miR-let-7d/e, mi699a-5p or negative control.

tag: tissue

tag: mouse id

tag: cell type

value: blastomeres

tag: genotype

value: WT

tag: treatment


title: Control eCLIP from K562 (ENCLB933YGK)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR720EEM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against TARDBP
experiment encode accession: ENCSR720EEM
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB933YGK
fragmentation methods: see document
size range: 175-300

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Gene Yeo, UCSD

tag: source

value: ATCC

tag: passage number

tag: link

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: snRNA-seq from heart left ventricle (ENCLB328JIP)

description:
https://www.encodeproject.org/experiments/ENCSR481QQR/
***************
biological replicate number: 1
technical replicate number: 1
description: snRNA on human heart left ventricle. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR131DKN)
experiment encode accession: ENCSR481QQR
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB328JIP
size range: 300-600
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (46 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: DM:no; HTN:no; CAD:no

value: 46 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS196UFN at ENCODE; https://www.encodeproject.org/ENCBS196UFN/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: Rrm4-Gfp iCLIP2 replicate 3

tag: strain

value: hyphae

value: wildtype expressing the RBP Rrm4 with C-terminal GFP tag

value: switch from yeast to hyphal growth

tag: time

value: 6 hours post hyphal induction


title: Rrm4-Gfp iCLIP2 replicate 5


title: IVF_Let7d_scRNA-seq_B3

tag: tissue

tag: mouse id

value: blastomeres

value: WT


title: Rrm4-Gfp iCLIP2 replicate 2

tag: cell type

tag: genotype


title: eCLIP from K562 (ENCLB043YOF)

description:
https://www.encodeproject.org/experiments/ENCSR720BJU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against TARDBP
experiment encode accession: ENCSR720BJU
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR720EEM
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB043YOF
fragmentation methods: see document
size range: 175-300

tag: antibody

value: TARDBP

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/


title: snRNA-seq from pancreas (ENCLB113GDH)

description:
https://www.encodeproject.org/experiments/ENCSR478FQR/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snATAC experiment (ENCSR690NZI).
experiment encode accession: ENCSR478FQR
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB113GDH
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (47 years) pancreas tissue, preserved by flash-freezing nuclear fraction

value: pancreas

value: tissue

tag: biosample encode accession

tag: Sex

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS941NVL at ENCODE; https://www.encodeproject.org/ENCBS941NVL/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: snRNA-seq from liver (ENCLB851FFF)

description:
https://www.encodeproject.org/experiments/ENCSR474DKO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR474DKO
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2023-03-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB851FFF
size range: 300-600

source_name: Homo sapiens male adult (35 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

tag: note

value: Homo sapiens liver tissue?

value: male

tag: health state

value: healthy

tag: dev stage

value: 35 year

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS538HCO at ENCODE; https://www.encodeproject.org/ENCBS538HCO/


title: IVF_Let7d_scRNA-seq_D2

value: blastomeres

value: WT

tag: treatment


title: IVF_Let7d_scRNA-seq_B2


title: Rrm4-Gfp iCLIP2 replicate 1

value: hyphae

value: wildtype expressing the RBP Rrm4 with C-terminal GFP tag

value: switch from yeast to hyphal growth

value: 6 hours post hyphal induction


title: eCLIP from K562 (ENCLB661XWS)

description:
https://www.encodeproject.org/experiments/ENCSR720BJU/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against TARDBP
experiment encode accession: ENCSR720BJU
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR720EEM
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB661XWS
fragmentation methods: see document
size range: 175-300

value: TARDBP

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

tag: age

value: 53 year

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: source

value: ATCC

tag: link

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: snRNA-seq from pancreas (ENCLB578ADC)

description:
https://www.encodeproject.org/experiments/ENCSR472RRP/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR229VVY).
experiment encode accession: ENCSR472RRP
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB578ADC
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (59 years) pancreas tissue, preserved by flash-freezing nuclear fraction

value: pancreas

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS828VFV at ENCODE; https://www.encodeproject.org/ENCBS828VFV/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: IVF_Let7d_scRNA-seq_B1

tag: tissue

tag: mouse id

tag: cell type

value: blastomeres

tag: genotype

value: WT

tag: strain


title: snRNA-seq from psoas muscle (ENCLB943WKY)

description:
https://www.encodeproject.org/experiments/ENCSR471YTA/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR000XQD).
experiment encode accession: ENCSR471YTA
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB943WKY
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female child (16 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

tag: biosample encode accession

tag: Sex

value: female

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: ENCBS880DIS at ENCODE; https://www.encodeproject.org/ENCBS880DIS/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: long read RNA-seq from layer of hippocampus (ENCLB543YEO)

description:
https://www.encodeproject.org/experiments/ENCSR038FOD/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_409, ENC4_410 hippocampus_B6Cast F1_PND10_3x female_4,5,6_ENC4_cDNA493
experiment encode accession: ENCSR038FOD
assay title: long read RNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB543YEO
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6CASTF1/J female (10 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

tag: description

tag: dev stage

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS739AAH at ENCODE; https://www.encodeproject.org/ENCBS739AAH/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from left cardiac atrium (ENCLB619VVF)

description:
https://www.encodeproject.org/experiments/ENCSR463EEP/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR491LSZ).
experiment encode accession: ENCSR463EEP
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB619VVF
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (60 years) left cardiac atrium tissue, preserved by flash-freezing nuclear fraction

value: left cardiac atrium

value: male

tag: health state

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS491YLC at ENCODE; https://www.encodeproject.org/ENCBS491YLC/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: Control eCLIP from HepG2 (ENCLB275PAJ)

description:
https://www.encodeproject.org/experiments/ENCSR240ZFU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DDX20
experiment encode accession: ENCSR240ZFU
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-28
lab: Gene Yeo, UCSD
library encode accession: ENCLB275PAJ
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

tag: line

value: cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: IVF_Let7d_scRNA-seq_C3

value: blastomeres

value: WT

tag: treatment


title: 70W-SM3-Luc2 cells, passage 18, rep 3

city: Albuquerque

first: Kathryn

last: Brayer

state: New Mexico

address: 1 University of New Mexico, MSC07 4025

institute: University of New Mexico

description: Ion S5XL buik RNAseq sample

data_processing:
Sequences were aligned using tmap (v5.10.11) to a BED file containing non-overlapping exons from UCSC genome hg38. Exon counts were calculated using HTseq (v0.11.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: uninjected CTC clonal cells

growth_protocol: Mice, growth protocol: Mice were injected with CTC cell line and monitored for 5-6 weeks. Tissues were isolated after necropsies and frozen for further RNA extraction. Once thawed, RNA was immediately extracted and sent for RNA Seq. Cell line, growth protocol: 70W-SM3 cells were brought up from LN2 and grown in 10%FBS, 90%DMEM. RNA was extracted in 2 days after thawing. Clinical samples: no growth protocol.

extract_protocol:
Total RNA was extracted from fractions using microRNA kit (Qiagen #74004)
Ribosomal RNA was removed using the RiboGone Kit, followed by cDNA synthesis using the SMARTer Universal Low Input RNA Kit for Sequencing (Takara Bio). Libraries were prepared using the Ion Plus Fragment Library Kit

treatment_protocol: No treatment

value: clone isolated from brain metastasis

tag: cell line

value: 70W-SM3-Luc2 cells, passage 20

value: melanoma

value: HLA A2.1

tag: time

value: Day 3

tag: processed data_aligner


title: Control eCLIP from K562 (ENCLB335WMG)

description:
https://www.encodeproject.org/experiments/ENCSR237YKY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against GARS
experiment encode accession: ENCSR237YKY
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB335WMG
fragmentation methods: see document
size range: 175-300

value: female

value: chronic myelogenous leukemia (CML)

value: adult

tag: age

value: 53 year

tag: lab

tag: source

value: ATCC

tag: passage number

tag: link

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: snRNA-seq from mucosa of descending colon (ENCLB611BAN)

description:
https://www.encodeproject.org/experiments/ENCSR460MGC/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR922FEK).
experiment encode accession: ENCSR460MGC
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB611BAN
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (61 years) mucosa of descending colon tissue, preserved by flash-freezing nuclear fraction

value: mucosa of descending colon

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS825JLE at ENCODE; https://www.encodeproject.org/ENCBS825JLE/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: IVF_Let7d_scRNA-seq_A2

tag: tissue

tag: mouse id

tag: cell type

value: blastomeres

tag: genotype

value: WT

tag: strain


title: Control eCLIP from K562 (ENCLB542ZZE)

description:
https://www.encodeproject.org/experiments/ENCSR237YKY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against GARS
experiment encode accession: ENCSR237YKY
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB542ZZE
fragmentation methods: see document
size range: 175-300

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: Gene Yeo, UCSD

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: 70W-SM3-Luc2 cells, passage 18, rep 1

description: Ion S5XL buik RNAseq sample

value: clone isolated from brain metastasis

tag: cell line

value: 70W-SM3-Luc2 cells, passage 18

value: melanoma

value: HLA A2.1

tag: time

value: Day 3

tag: processed data_aligner

value: i will do this


title: snRNA-seq from heart left ventricle (ENCLB460PSY)

description:
https://www.encodeproject.org/experiments/ENCSR455MGH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR455MGH
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB460PSY
size range: 300-600

source_name: Homo sapiens female adult (32 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: nonischemic (EF 14%, LVEDD 8.8)

value: adult

tag: age

value: 32 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Shin Lin

value: ENCBS655FSH at ENCODE; https://www.encodeproject.org/ENCBS655FSH/

value: Derived from ENCODE donor ENCDO739PAW; https://www.encodeproject.org/ENCDO739PAW/


title: Mo.6C.LPS.TREAT.Sp#3

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Spleen

extract_protocol:
At 2 hours post-injection, 1,000 cells of the 14 immune cell-types from spleen and peritoneal cavity were double-sorted in 5uL of TCL Buffer (QIAGEN) containing 1% 2-mercaptoethanol (Sigma) by BD FACS Aria. For a time-course profiling, 1,000 cells of monocytes and peritoneal macrophages were double-sorted at 2, 4, 8 and 24 hr post-injection  in 5uL of TCL Buffer containing 1% 2-mercaptoethanol and then processed for RNA-seq.
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf)

treatment_protocol: 5-8 week old C57Bl/6J mice shipped from the Jackson Laboratory, Bar Harbor. Mice were injected intravenously with either a free cytokine (5ug of IL1b, IL6 or TNFa in 120uL of PBS) , PBS (120uL) or LPS (1ng in 120uL of PBS).

tag: tissue

value: Spleen

value: Mo

tag: treatment

value: LPS


title: snRNA-seq from pancreas (ENCLB357XZN)

description:
https://www.encodeproject.org/experiments/ENCSR445LCA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR445LCA
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB357XZN
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (41 years) pancreas tissue, preserved by flash-freezing nuclear fraction

value: pancreas

value: female

value: DM:no; HTN:no; CAD:no

value: 41 year

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: not applicable

tag: link

value: ENCBS630XPX at ENCODE; https://www.encodeproject.org/ENCBS630XPX/


title: Control eCLIP from HepG2 (ENCLB705FGH)

description:
https://www.encodeproject.org/experiments/ENCSR224ECB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against RPL23A
experiment encode accession: ENCSR224ECB
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-12-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB705FGH
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

tag: biosample encode accession

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: CTCs from blood, day 0, rep 6

description: Ion S5XL buik RNAseq sample

source_name: 1st gen NSG blood

value: blood

value: no

tag: cell type

value: melanoma

tag: genotype

value: HLA A2.1

value: Day 0

value: i will do this


title: Control eCLIP from K562 (ENCLB238MYZ)

description:
https://www.encodeproject.org/experiments/ENCSR219TIG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SRSF9
experiment encode accession: ENCSR219TIG
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB238MYZ
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: dev stage

value: adult

value: 53 year

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: Mo.6C.LPS.TREAT.Sp#2

value: Spleen

value: Mo

tag: strain

value: LPS


title: Control eCLIP from K562 (ENCLB558WWD)

description:
https://www.encodeproject.org/experiments/ENCSR219TIG/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against SRSF9
experiment encode accession: ENCSR219TIG
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB558WWD
fragmentation methods: see document
size range: 175-300

value: cell line

value: Gene Yeo, UCSD

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: snRNA-seq from heart right ventricle (ENCLB765NUA)

description:
https://www.encodeproject.org/experiments/ENCSR426PDU/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR169BCG).
experiment encode accession: ENCSR426PDU
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB765NUA
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (41 years) heart right ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart right ventricle

value: tissue

value: DM:no; HTN:no; CAD:no

tag: age

value: 41 year

tag: lab

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS735VCK at ENCODE; https://www.encodeproject.org/ENCBS735VCK/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: CTCs from blood, day 0, rep 5

description: Ion S5XL buik RNAseq sample

tag: tissue

value: blood

tag: cell line

value: no

value: melanoma

value: HLA A2.1

tag: time

value: Day 0

tag: processed data_aligner

value: i will do this


title: Mo.6C.LPS.TREAT.Sp#1

value: Spleen

value: Mo

tag: treatment

value: LPS


title: CTCs from blood, day 0, rep 4

description: Ion S5XL buik RNAseq sample

source_name: 2nd gen HuNBSGW blood


title: Control eCLIP from K562 (ENCLB885HLI)

description:
https://www.encodeproject.org/experiments/ENCSR701KRV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RPS10
experiment encode accession: ENCSR701KRV
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB885HLI
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

tag: biosample encode accession

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: IVF_Let7d_scRNA-seq_A3

tag: mouse id

tag: cell type

value: blastomeres

tag: genotype

value: WT


title: Mo.6C.LPS.CTRL.Sp#3

value: PBS


title: CTCs from blood, day 0, rep 3

description: Ion S5XL buik RNAseq sample

value: blood

value: no

value: melanoma

value: HLA A2.1

value: Day 0


title: Mo.6C.LPS.CTRL.Sp#2

value: Spleen

value: Mo


title: Control eCLIP from K562 (ENCLB094ANL)

description:
https://www.encodeproject.org/experiments/ENCSR701KRV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against RPS10
experiment encode accession: ENCSR701KRV
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB094ANL
fragmentation methods: see document
size range: 175-300

value: cell line

tag: dev stage

value: adult

tag: Sex

value: female

value: 53 year

tag: health state

tag: passage number

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/


title: snRNA-seq from heart left ventricle (ENCLB181TPV)

description:
https://www.encodeproject.org/experiments/ENCSR405YKM/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR318ERF).
experiment encode accession: ENCSR405YKM
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB181TPV
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (59 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: DM:yes; HTN:yes; CAD:no

tag: age

value: 59 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

value: ENCBS544NEM at ENCODE; https://www.encodeproject.org/ENCBS544NEM/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: CTCs from blood, day 0, rep 2

description: Ion S5XL buik RNAseq sample

tag: tissue

value: blood

tag: cell line

value: no

value: melanoma

value: HLA A2.1

value: Day 0


title: IVF_Let7d_scRNA-seq_A1

value: blastomeres

value: WT

tag: strain


title: 70W-SM3-Luc2 cells, passage 18, rep 2

description: Ion S5XL buik RNAseq sample

value: clone isolated from brain metastasis

value: 70W-SM3-Luc2 cells, passage 19

tag: time

value: Day 3

tag: processed data_aligner


title: eCLIP from K562 (ENCLB630NXD)

description:
https://www.encodeproject.org/experiments/ENCSR448GXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against GARS
experiment encode accession: ENCSR448GXJ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR237YKY
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB630NXD
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

tag: antibody

value: GARS

tag: line

value: cell line

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

tag: lab

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Mo.6C.LPS.CTRL.Sp#1

value: Spleen

tag: cell type

value: Mo

tag: treatment

value: PBS


title: CTCs from blood, day 0, rep 1

description: Ion S5XL buik RNAseq sample

value: blood

value: no

value: melanoma

tag: genotype

value: HLA A2.1

value: Day 0


title: snRNA-seq from heart left ventricle (ENCLB593ESF)

description:
https://www.encodeproject.org/experiments/ENCSR398YBK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR398YBK
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB593ESF
size range: 300-600

source_name: Homo sapiens female adult (48 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

tag: Sex

tag: dev stage

value: 48 year

value: Michael Snyder, Stanford

value: Shin Lin

tag: health state

value: healthy

tag: link

value: ENCBS078WTV at ENCODE; https://www.encodeproject.org/ENCBS078WTV/

value: Derived from ENCODE donor ENCDO817MDD; https://www.encodeproject.org/ENCDO817MDD/


title: MF.TNFa.2hr.PC#2

source_name: Peritoneal Cavity

tag: tissue

value: Peritoneal Cavity

value: MFpc

value: TNFa


title: liver cells, day 0, rep 3

description: Ion S5XL buik RNAseq sample

source_name: 2nd gen liver

value: liver

tag: cell line


title: snRNA-seq from heart left ventricle (ENCLB103OKD)

description:
https://www.encodeproject.org/experiments/ENCSR439ZVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR439ZVQ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB103OKD
fragmentation methods: see document
size range: 300-600

source_name: Homo sapiens male adult (20 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: male

value: nonischemic

value: adult

tag: age

value: 20 year

tag: subcellular fraction term name

value: nucleus

tag: source

value: ENCBS650GQB at ENCODE; https://www.encodeproject.org/ENCBS650GQB/

value: Derived from ENCODE donor ENCDO061UFT; https://www.encodeproject.org/ENCDO061UFT/


title: eCLIP from K562 (ENCLB505WYK)

description:
https://www.encodeproject.org/experiments/ENCSR448GXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against GARS
experiment encode accession: ENCSR448GXJ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR237YKY
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB505WYK
fragmentation methods: see document
size range: 175-300

tag: antibody

value: GARS

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: eCLIP from HepG2 (ENCLB233ERR)

description:
https://www.encodeproject.org/experiments/ENCSR187VEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against TARDBP
experiment encode accession: ENCSR187VEQ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR265LJL
encode release date: 2022-12-17
lab: Gene Yeo, UCSD
library encode accession: ENCLB233ERR
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: TARDBP

tag: line

tag: biosample encode accession

value: hepatocellular carcinoma

value: child

value: 15 year

tag: lab

value: ENCBS133LVQ at ENCODE; https://www.encodeproject.org/ENCBS133LVQ/


title: liver cells, day 0, rep 2

description: Ion S5XL buik RNAseq sample

value: liver

value: no

tag: cell type

value: melanoma

tag: genotype

value: HLA A2.1

tag: time

value: Day 0

tag: processed data_aligner


title: snRNA-seq from left lobe of liver (ENCLB335ITX)

description:
https://www.encodeproject.org/experiments/ENCSR369UFT/
***************
biological replicate number: 1
technical replicate number: 1
description: snRNA on left lobe of liver. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR139ATR).
experiment encode accession: ENCSR369UFT
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB335ITX
size range: 300-600
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (45 years) left lobe of liver tissue nuclear fraction

value: left lobe of liver

value: tissue

tag: Sex

value: male

tag: health state

value: DM:no; HTN:yes; CAD:no

tag: dev stage

value: adult

value: 45 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS344HUA at ENCODE; https://www.encodeproject.org/ENCBS344HUA/

value: Derived from ENCODE donor ENCDO757VPQ; https://www.encodeproject.org/ENCDO757VPQ/


title: eCLIP from HepG2 (ENCLB139SPG)

description:
https://www.encodeproject.org/experiments/ENCSR187VEQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against TARDBP
experiment encode accession: ENCSR187VEQ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR265LJL
encode release date: 2022-12-17
lab: Gene Yeo, UCSD
library encode accession: ENCLB139SPG
fragmentation methods: see document
size range: 175-300

value: TARDBP

value: cell line

value: hepatocellular carcinoma

value: child

tag: age

value: 15 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS768GCL at ENCODE; https://www.encodeproject.org/ENCBS768GCL/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: snRNA-seq from right lobe of liver (ENCLB151JZY)

description:
https://www.encodeproject.org/experiments/ENCSR367YUX/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR630YEA).
experiment encode accession: ENCSR367YUX
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB151JZY
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (47 years) right lobe of liver tissue, preserved by flash-freezing nuclear fraction

value: right lobe of liver

value: tissue

value: female

value: DM:no; HTN:yes; CAD:no

value: 47 year

tag: subcellular fraction term name

tag: source

value: ENCBS375LMS at ENCODE; https://www.encodeproject.org/ENCBS375LMS/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: MF.TNFa.4hr.PC#2

tag: tissue

value: Peritoneal Cavity

value: MFpc

tag: strain

tag: treatment

value: TNFa


title: snRNA-seq from heart (ENCLB942EHW)

description:
https://www.encodeproject.org/experiments/ENCSR409CQM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR409CQM
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2024-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB942EHW
size range: 300-600

source_name: Homo sapiens male embryo (59 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

tag: note

value: Homo sapiens heart tissue

value: male

value: embryonic

value: 59 day

value: Michael Snyder, Stanford

value: nucleus

value: BDRL

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS092RCN at ENCODE; https://www.encodeproject.org/ENCBS092RCN/


title: Control eCLIP from K562 (ENCLB411WSR)

description:
https://www.encodeproject.org/experiments/ENCSR181YHI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against METTL1
experiment encode accession: ENCSR181YHI
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2023-01-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB411WSR
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

tag: passage number

tag: lab

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: MF.TNFa.4hr.PC#1

value: Peritoneal Cavity

tag: cell type

value: MFpc

value: TNFa


title: snRNA-seq from adrenal gland (ENCLB943KZN)

description:
https://www.encodeproject.org/experiments/ENCSR362YDM/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR420EWQ).
experiment encode accession: ENCSR362YDM
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB943KZN
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (26 years) adrenal gland tissue, preserved by flash-freezing nuclear fraction

value: adrenal gland

value: tissue

tag: Sex

value: male

tag: health state

value: DM:no; HTN:no; CAD:no

value: 26 year

value: Yiing Lin, MD, PhD

value: ENCBS099KRU at ENCODE; https://www.encodeproject.org/ENCBS099KRU/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: brain cells, day 0, rep 9

description: Ion S5XL buik RNAseq sample

source_name: 2nd gen HuNBSGW brain from blood group

value: brain

tag: cell line

value: no

value: melanoma

tag: genotype

value: HLA A2.1

tag: time

value: Day 0

tag: processed data_aligner


title: Control eCLIP from K562 (ENCLB641DVY)

description:
https://www.encodeproject.org/experiments/ENCSR181YHI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against METTL1
experiment encode accession: ENCSR181YHI
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2023-01-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB641DVY
fragmentation methods: see document
size range: 175-300

value: cell line

tag: dev stage

value: adult

value: female

tag: age

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

tag: link

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: snRNA-seq from ovary (ENCLB932FNN)

description:
https://www.encodeproject.org/experiments/ENCSR362HUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR362HUP
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB932FNN
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (41 years) ovary tissue, preserved by flash-freezing nuclear fraction

value: ovary

value: tissue

value: DM:no; HTN:no; CAD:no

value: 41 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

value: ENCBS034EPW at ENCODE; https://www.encodeproject.org/ENCBS034EPW/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: MF.TNFa.8hr.PC#2

tag: tissue

value: Peritoneal Cavity

value: MFpc

tag: strain

tag: treatment

value: TNFa


title: eCLIP from K562 (ENCLB808PTW)

description:
https://www.encodeproject.org/experiments/ENCSR179MPN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RYBP
experiment encode accession: ENCSR179MPN
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR407QDZ
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB808PTW
fragmentation methods: see document
size range: 175-300

tag: antibody

value: RYBP

tag: line

value: cell line

tag: biosample encode accession

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: passage number

value: Gene Yeo, UCSD


title: brain cells, day 0, rep 8

description: Ion S5XL buik RNAseq sample

source_name: 2nd gen HuNBSGW brain from brain group

value: brain

value: no

tag: cell type

value: melanoma

value: HLA A2.1

value: Day 0


title: MF.TNFa.8hr.PC#1


title: brain cells, day 0, rep 7

description: Ion S5XL buik RNAseq sample

tag: cell line


title: eCLIP from K562 (ENCLB477WMP)

description:
https://www.encodeproject.org/experiments/ENCSR179MPN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RYBP
experiment encode accession: ENCSR179MPN
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR407QDZ
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB477WMP
fragmentation methods: see document
size range: 175-300

tag: Sex

tag: health state

tag: lab

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: snRNA-seq from heart left ventricle (ENCLB243NMQ)

description:
https://www.encodeproject.org/experiments/ENCSR352DXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR352DXB
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB243NMQ
fragmentation methods: see document
size range: 300-600

source_name: Homo sapiens male adult (57 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: male

value: nonischemic

tag: dev stage

tag: age

value: 57 year

value: Michael Snyder, Stanford

value: nucleus

value: Shin Lin

tag: link

value: ENCBS159AKG at ENCODE; https://www.encodeproject.org/ENCBS159AKG/

value: Derived from ENCODE donor ENCDO639HZG; https://www.encodeproject.org/ENCDO639HZG/


title: snRNA-seq from right lobe of liver (ENCLB065ONF)

description:
https://www.encodeproject.org/experiments/ENCSR398PIW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR398PIW
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB065ONF
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (45 years) right lobe of liver tissue nuclear fraction

value: right lobe of liver

value: DM:no; HTN:yes; CAD:no

value: adult

value: 45 year

tag: subcellular fraction term name

tag: source

value: Yiing Lin, MD, PhD

value: ENCBS439NNJ at ENCODE; https://www.encodeproject.org/ENCBS439NNJ/


title: snRNA-seq from heart left ventricle (ENCLB218CWN)

description:
https://www.encodeproject.org/experiments/ENCSR349AHE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR349AHE
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB218CWN
size range: 300-600

source_name: Homo sapiens male adult (45 years) heart left ventricle tissue, preserved by flash-freezing

tag: description

value: Homo sapiens heart left ventricle tissue

value: healthy

value: ENCBS042LKH at ENCODE; https://www.encodeproject.org/ENCBS042LKH/

value: Derived from ENCODE donor ENCDO894OKI; https://www.encodeproject.org/ENCDO894OKI/


title: eCLIP from K562 (ENCLB079TTR)

description:
https://www.encodeproject.org/experiments/ENCSR168VUE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against MORC2
experiment encode accession: ENCSR168VUE
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR790SPV
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB079TTR
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

value: cell line

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: snRNA-seq from heart left ventricle (ENCLB793KIA)

description:
https://www.encodeproject.org/experiments/ENCSR345CVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR345CVL
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB793KIA
size range: 300-600

source_name: Homo sapiens male adult (37 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: male

value: adult

value: 37 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS183VKV at ENCODE; https://www.encodeproject.org/ENCBS183VKV/

value: Derived from ENCODE donor ENCDO123GXG; https://www.encodeproject.org/ENCDO123GXG/


title: brain cells, day 0, rep 5

description: Ion S5XL buik RNAseq sample

tag: tissue

value: brain

value: no

value: melanoma

tag: genotype

value: HLA A2.1

tag: time

value: Day 0

tag: processed data_aligner


title: MF.TNFa.24hr.PC#1

value: Peritoneal Cavity

tag: cell type

value: MFpc

tag: strain

tag: treatment

value: TNFa


title: brain cells, day 0, rep 6

description: Ion S5XL buik RNAseq sample

tag: cell line


title: MF.PBS.24hr.PC#2

value: PBS


title: liver cells, day 0, rep 1

description: Ion S5XL buik RNAseq sample

value: liver


title: MF.TNFa.2hr.PC#1


title: snRNA-seq from natural killer cell (ENCLB831IHU)

description:
https://www.encodeproject.org/experiments/ENCSR337HKS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337HKS
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB831IHU
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (33 years) natural killer primary cell nuclear fraction

value: natural killer cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

value: 33 year

tag: lab

value: Yijun Ruan, JAX

value: nucleus

value: AllCells

value: ENCBS650RYP at ENCODE; https://www.encodeproject.org/ENCBS650RYP/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: brain cells, day 0, rep 4

description: Ion S5XL buik RNAseq sample

value: brain

value: no

value: melanoma


title: snRNA-seq from heart left ventricle (ENCLB461YMD)

description:
https://www.encodeproject.org/experiments/ENCSR328GTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328GTN
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB461YMD
size range: 300-600

source_name: Homo sapiens male adult (68 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: health state

value: ischemic

tag: dev stage

value: adult

tag: age

value: 68 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS437OBX at ENCODE; https://www.encodeproject.org/ENCBS437OBX/

value: Derived from ENCODE donor ENCDO184BIH; https://www.encodeproject.org/ENCDO184BIH/


title: MF.PBS.24hr.PC#1

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: MFpc

value: PBS


title: brain cells, day 0, rep 3

description: Ion S5XL buik RNAseq sample

value: HLA A2.1

value: Day 0


title: eCLIP from K562 (ENCLB543ZUO)

description:
https://www.encodeproject.org/experiments/ENCSR168VUE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against MORC2
experiment encode accession: ENCSR168VUE
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR790SPV
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB543ZUO
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

tag: source

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: Mo.6C.TNFa.2hr.Sp#2

source_name: Spleen

tag: tissue

value: Spleen

value: Mo

value: TNFa


title: snRNA-seq from ovary (ENCLB814OYP)

description:
https://www.encodeproject.org/experiments/ENCSR298MPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298MPV
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB814OYP
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (47 years) ovary tissue, preserved by flash-freezing nuclear fraction

value: ovary

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 47 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS980YMW at ENCODE; https://www.encodeproject.org/ENCBS980YMW/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: brain cells, day 0, rep 2

description: Ion S5XL buik RNAseq sample

value: brain

value: no

tag: cell type

value: melanoma

tag: genotype

value: HLA A2.1

tag: time

value: Day 0

tag: processed data_aligner


title: Mo.6C.TNFa.2hr.Sp#1

value: Spleen

value: Mo

tag: strain

tag: treatment


title: Control eCLIP from K562 (ENCLB444WJE)

description:
https://www.encodeproject.org/experiments/ENCSR143CTS/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPK
experiment encode accession: ENCSR143CTS
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB444WJE
fragmentation methods: see document
size range: 175-300

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

tag: lab

value: Gene Yeo, UCSD

value: ATCC

value: not applicable

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: snRNA-seq from ovary (ENCLB674XYV)

description:
https://www.encodeproject.org/experiments/ENCSR297ZTQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR297ZTQ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB674XYV
fragmentation methods: none
size range: 150-1000

source_name: Homo sapiens female adult (61 years) ovary tissue, preserved by flash-freezing nuclear fraction

value: ovary

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

tag: dev stage

value: adult

tag: age

value: 61 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS720BUN at ENCODE; https://www.encodeproject.org/ENCBS720BUN/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: brain cells, day 0, rep 1

description: Ion S5XL buik RNAseq sample

value: brain

tag: cell line

value: no

value: melanoma

value: HLA A2.1

value: Day 0


title: MF.TNFa.24hr.PC#2

value: Peritoneal Cavity

value: MFpc

value: TNFa


title: Control eCLIP from K562 (ENCLB550YVG)

description:
https://www.encodeproject.org/experiments/ENCSR143CTS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPK
experiment encode accession: ENCSR143CTS
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB550YVG
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: snRNA-seq from liver (ENCLB823WAF)

description:
https://www.encodeproject.org/experiments/ENCSR292BJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR292BJF
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2023-03-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB823WAF
size range: 300-600

source_name: Homo sapiens male adult (45 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: tissue

tag: note

value: Homo sapiens liver tissue?

value: male

value: healthy

value: adult

value: 45 year

value: Michael Snyder, Stanford

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS475QWU at ENCODE; https://www.encodeproject.org/ENCBS475QWU/


title: Mo.6C.TNFa.4hr.Sp#2

tag: tissue

value: Spleen

tag: cell type

value: Mo

value: TNFa


title: snRNA-seq from layer of hippocampus (ENCLB835IXS)

description:
https://www.encodeproject.org/experiments/ENCSR995ZKH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR995ZKH
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB835IXS
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: not collected

tag: subcellular fraction term name

value: The Jackson Laboratory

value: ENCBS818LEG at ENCODE; https://www.encodeproject.org/ENCBS818LEG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: eCLIP from K562 (ENCLB604AQS)

description:
https://www.encodeproject.org/experiments/ENCSR100ARZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RPS6
experiment encode accession: ENCSR100ARZ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR911RWF
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB604AQS
fragmentation methods: see document
size range: 175-300

tag: antibody

value: cell line

tag: biosample encode accession

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: snRNA-seq from liver (ENCLB566WWJ)

description:
https://www.encodeproject.org/experiments/ENCSR291IHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291IHH
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2023-03-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB566WWJ
size range: 300-600

source_name: Homo sapiens male adult (18 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: tissue

value: Homo sapiens liver tissue?

tag: Sex

value: male

tag: health state

value: healthy

value: adult

value: 18 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: not applicable

value: ENCBS882OYS at ENCODE; https://www.encodeproject.org/ENCBS882OYS/


title: snRNA-seq from adrenal gland (ENCLB568RWC)

description:
https://www.encodeproject.org/experiments/ENCSR988AMY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR988AMY
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB568RWC
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue, preserved by flash-freezing nuclear fraction

value: adrenal gland

value: not collected

tag: dev stage

tag: lab

value: The Jackson Laboratory

value: ENCBS238PJP at ENCODE; https://www.encodeproject.org/ENCBS238PJP/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Mo.6C.TNFa.4hr.Sp#1

value: Spleen

value: Mo

tag: strain

tag: treatment

value: TNFa


title: Mo.6C.TNFa.8hr.Sp#2


title: eCLIP from K562 (ENCLB327WKM)

description:
https://www.encodeproject.org/experiments/ENCSR090LNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ELAVL1
experiment encode accession: ENCSR090LNQ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR327BBW
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB327WKM
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

tag: age

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: eCLIP from K562 (ENCLB097RVP)

description:
https://www.encodeproject.org/experiments/ENCSR153STI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RNF187
experiment encode accession: ENCSR153STI
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR254NWE
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB097RVP
fragmentation methods: see document
size range: 175-300

value: adult

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: eCLIP from K562 (ENCLB076RMX)

description:
https://www.encodeproject.org/experiments/ENCSR100ARZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RPS6
experiment encode accession: ENCSR100ARZ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR911RWF
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB076RMX
fragmentation methods: see document
size range: 175-300

tag: source

tag: collection date

value: not applicable


title: snRNA-seq from heart (ENCLB953VEF)

description:
https://www.encodeproject.org/experiments/ENCSR288WET/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR288WET
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2024-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB953VEF
size range: 300-600

source_name: Homo sapiens female embryo (127 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: tissue

tag: note

value: Homo sapiens heart tissue

value: embryonic

value: 127 day

value: Michael Snyder, Stanford

value: nucleus

value: BDRL

tag: geographic location

tag: link

value: ENCBS869CTV at ENCODE; https://www.encodeproject.org/ENCBS869CTV/


title: snRNA-seq from left colon (ENCLB280ZGL)

description:
https://www.encodeproject.org/experiments/ENCSR289ANH/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR830FPR).
experiment encode accession: ENCSR289ANH
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB280ZGL
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (59 years) left colon tissue, preserved by flash-freezing nuclear fraction

value: left colon

value: female

value: DM:yes; HTN:yes; CAD:no

value: 59 year

tag: subcellular fraction term name

value: Yiing Lin, MD, PhD

value: ENCBS451VLL at ENCODE; https://www.encodeproject.org/ENCBS451VLL/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: snRNA-seq from layer of hippocampus (ENCLB104XFX)

description:
https://www.encodeproject.org/experiments/ENCSR987SOK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR987SOK
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB104XFX
fragmentation methods: see document
size range: 300-600

value: layer of hippocampus

value: not collected

value: The Jackson Laboratory

value: ENCBS502QAA at ENCODE; https://www.encodeproject.org/ENCBS502QAA/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: eCLIP from K562 (ENCLB739TEB)

description:
https://www.encodeproject.org/experiments/ENCSR090LNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ELAVL1
experiment encode accession: ENCSR090LNQ
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR327BBW
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB739TEB
fragmentation methods: see document
size range: 175-300

tag: antibody

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Mo.6C.TNFa.24hr.Sp#2

tag: tissue

value: Spleen

tag: cell type

value: Mo

value: TNFa


title: snRNA-seq from layer of hippocampus (ENCLB850RYI)

description:
https://www.encodeproject.org/experiments/ENCSR968RPR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR968RPR
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB850RYI
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue, preserved by flash-freezing nuclear fraction

value: tissue

tag: biosample encode accession

tag: Sex

value: Michael Snyder, Stanford

value: nucleus

value: ENCBS841ZQP at ENCODE; https://www.encodeproject.org/ENCBS841ZQP/


title: snRNA-seq from psoas muscle (ENCLB513JLQ)

description:
https://www.encodeproject.org/experiments/ENCSR281RIH/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR869LEV).
experiment encode accession: ENCSR281RIH
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB513JLQ
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (59 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

value: female

tag: health state

value: DM:yes; HTN:yes; CAD:no

tag: dev stage

value: 59 year

tag: lab

value: Yiing Lin, MD, PhD

value: ENCBS865RKW at ENCODE; https://www.encodeproject.org/ENCBS865RKW/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: Mo.6C.TNFa.24hr.Sp#1

tag: strain

tag: treatment


title: Control eCLIP from K562 (ENCLB578HCK)

description:
https://www.encodeproject.org/experiments/ENCSR060MRW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against MBNL1
experiment encode accession: ENCSR060MRW
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB578HCK
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

tag: age

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

tag: passage number


title: snRNA-seq from pancreas (ENCLB063JPD)

description:
https://www.encodeproject.org/experiments/ENCSR281NBH/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR868CRK).
experiment encode accession: ENCSR281NBH
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB063JPD
fragmentation methods: none
size range: 150-1000

source_name: Homo sapiens female child (16 years) pancreas tissue, preserved by flash-freezing nuclear fraction

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

tag: source

value: ENCBS928ZLX at ENCODE; https://www.encodeproject.org/ENCBS928ZLX/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: Control eCLIP from K562 (ENCLB475UJU)

description:
https://www.encodeproject.org/experiments/ENCSR060MRW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against MBNL1
experiment encode accession: ENCSR060MRW
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB475UJU
fragmentation methods: see document
size range: 175-300

value: female

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: snRNA-seq from layer of hippocampus (ENCLB012QYK)

description:
https://www.encodeproject.org/experiments/ENCSR944XPC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR944XPC
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB012QYK
fragmentation methods: see document
size range: 300-600

value: layer of hippocampus

value: not collected

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: The Jackson Laboratory

tag: link

value: ENCBS282ICD at ENCODE; https://www.encodeproject.org/ENCBS282ICD/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from adrenal gland (ENCLB139QES)

description:
https://www.encodeproject.org/experiments/ENCSR908CQZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908CQZ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB139QES
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue nuclear fraction

value: adrenal gland

value: ENCBS669LEM at ENCODE; https://www.encodeproject.org/ENCBS669LEM/


title: Mo.6C.PBS.24hr.Sp#2

tag: tissue

value: Spleen

value: Mo

value: PBS


title: eCLIP from K562 (ENCLB845KZM)

description:
https://www.encodeproject.org/experiments/ENCSR153STI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RNF187
experiment encode accession: ENCSR153STI
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR254NWE
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB845KZM
fragmentation methods: see document
size range: 175-300

tag: antibody

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: snRNA-seq from heart (ENCLB589DNC)

description:
https://www.encodeproject.org/experiments/ENCSR268GBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR268GBA
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2024-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB589DNC
size range: 300-600

source_name: Homo sapiens female embryo (73 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: tissue

tag: biosample encode accession

tag: note

value: Homo sapiens heart tissue

value: female

value: embryonic

value: 73 day

value: Michael Snyder, Stanford

value: BDRL

value: not applicable

value: ENCBS539UEJ at ENCODE; https://www.encodeproject.org/ENCBS539UEJ/


title: snRNA-seq from gastrocnemius (ENCLB995TFV)

description:
https://www.encodeproject.org/experiments/ENCSR835ZXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR835ZXV
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB995TFV
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J gastrocnemius tissue nuclear fraction

value: gastrocnemius

tag: Sex

value: not collected

value: nucleus

value: The Jackson Laboratory

value: ENCBS911KWK at ENCODE; https://www.encodeproject.org/ENCBS911KWK/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Mo.6C.PBS.24hr.Sp#1

value: Spleen

tag: cell type

value: Mo

value: PBS


title: Mo.6C.TNFa.8hr.Sp#1

value: TNFa


title: snRNA-seq from layer of hippocampus (ENCLB089YWN)

description:
https://www.encodeproject.org/experiments/ENCSR835JFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR835JFN
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB089YWN
fragmentation methods: see document
size range: 300-600

value: layer of hippocampus

value: tissue

tag: dev stage

tag: lab

value: ENCBS192DDF at ENCODE; https://www.encodeproject.org/ENCBS192DDF/


title: Control eCLIP from K562 (ENCLB904DTL)

description:
https://www.encodeproject.org/experiments/ENCSR058PIY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX47
experiment encode accession: ENCSR058PIY
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB904DTL
fragmentation methods: see document
size range: 175-300

value: cell line

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: snRNA-seq from right lobe of liver (ENCLB038DYV)

description:
https://www.encodeproject.org/experiments/ENCSR261LPM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR261LPM
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB038DYV
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (40 years) right lobe of liver tissue nuclear fraction

value: right lobe of liver

value: male

value: DM:no; HTN:yes; CAD:no

value: 40 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: not applicable

value: ENCBS015LZE at ENCODE; https://www.encodeproject.org/ENCBS015LZE/


title: B.fo.TNFa.Sp_3

source_name: Peritoneal Cavity

extract_protocol:
At 2 hours post-injection, 1,000 cells of the 14 immune cell-types from spleen and peritoneal cavity were double-sorted in 5uL of TCL Buffer (QIAGEN) containing 1% 2-mercaptoethanol (Sigma) by BD FACS Aria
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf)

treatment_protocol: 5-8 week old C57Bl/6J mice shipped from the Jackson Laboratory, Bar Harbor. Mice were injected intravenously with either a free cytokine (5ug of IL1b, IL6 or TNFa in 120uL of PBS)  or PBS (120uL).

value: Peritoneal Cavity

tag: strain

tag: treatment

value: TNFa


title: snRNA-seq from gastrocnemius (ENCLB275WWO)

description:
https://www.encodeproject.org/experiments/ENCSR771MOE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR771MOE
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB275WWO
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J male (2 months) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

tag: description

value: Encode B6CastF1 2 months male #2 Gastroc

value: not collected

tag: age

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS969HWV at ENCODE; https://www.encodeproject.org/ENCBS969HWV/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: eCLIP from K562 (ENCLB705DYM)

description:
https://www.encodeproject.org/experiments/ENCSR008MQM/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DDX43
experiment encode accession: ENCSR008MQM
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR816TOM
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB705DYM
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

tag: source

value: ATCC

tag: collection date

value: ENCBS592SHU at ENCODE; https://www.encodeproject.org/ENCBS592SHU/


title: B.fo.TNFa.Sp_2

tag: tissue

value: Peritoneal Cavity

value: TNFa


title: snRNA-seq from pancreas (ENCLB774YSO)

description:
https://www.encodeproject.org/experiments/ENCSR261BXB/
***************
biological replicate number: 1
technical replicate number: 1
description: snRNA on human pancreas. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR496XXB).
experiment encode accession: ENCSR261BXB
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB774YSO
size range: 300-600
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (26 years) pancreas tissue, preserved by flash-freezing nuclear fraction

value: pancreas

value: tissue

value: male

value: DM:no; HTN:no; CAD:no

value: 26 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS995XKZ at ENCODE; https://www.encodeproject.org/ENCBS995XKZ/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: eCLIP from K562 (ENCLB505KRK)

description:
https://www.encodeproject.org/experiments/ENCSR008MQM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DDX43
experiment encode accession: ENCSR008MQM
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR816TOM
encode release date: 2022-11-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB505KRK
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

value: cell line

tag: biosample encode accession

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: B.fo.TNFa.Sp_1

value: Peritoneal Cavity

tag: cell type

value: TNFa


title: snRNA-seq from heart left ventricle (ENCLB043KZW)

description:
https://www.encodeproject.org/experiments/ENCSR259VOY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR259VOY
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB043KZW
fragmentation methods: see document
size range: 300-600

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

tag: Sex

value: male

value: ischemic

tag: dev stage

value: 54 year

value: Shin Lin

value: ENCBS034WRO at ENCODE; https://www.encodeproject.org/ENCBS034WRO/

value: Derived from ENCODE donor ENCDO874YWU; https://www.encodeproject.org/ENCDO874YWU/


title: snRNA-seq from layer of hippocampus (ENCLB225KMP)

description:
https://www.encodeproject.org/experiments/ENCSR742NWO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR742NWO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB225KMP
fragmentation methods: see document
size range: 300-600

value: layer of hippocampus

value: not collected

tag: lab

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS749FCK at ENCODE; https://www.encodeproject.org/ENCBS749FCK/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: B.fo.IL6.Sp_2

value: Peritoneal Cavity

tag: strain


title: snRNA-seq from heart right ventricle (ENCLB643HGB)

description:
https://www.encodeproject.org/experiments/ENCSR258SZI/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR681OLJ).
experiment encode accession: ENCSR258SZI
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB643HGB
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (59 years) heart right ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart right ventricle

value: female

tag: health state

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 59 year

value: Yiing Lin, MD, PhD

value: ENCBS391QZV at ENCODE; https://www.encodeproject.org/ENCBS391QZV/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: snRNA-seq from heart left ventricle (ENCLB610ELT)

description:
https://www.encodeproject.org/experiments/ENCSR273JWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273JWD
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB610ELT
size range: 300-600

source_name: Homo sapiens male adult (39 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: male

value: healthy

value: 39 year

value: Shin Lin

value: ENCBS671QYO at ENCODE; https://www.encodeproject.org/ENCBS671QYO/

value: Derived from ENCODE donor ENCDO266KDE; https://www.encodeproject.org/ENCDO266KDE/


title: snRNA-seq from left cerebral cortex (ENCLB676AMA)

description:
https://www.encodeproject.org/experiments/ENCSR720TUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR720TUP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB676AMA
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: not collected

tag: age

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS512ZAC at ENCODE; https://www.encodeproject.org/ENCBS512ZAC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: eCLIP from K562 (ENCLB383UAZ)

description:
https://www.encodeproject.org/experiments/ENCSR004VIR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against EEF2
experiment encode accession: ENCSR004VIR
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR344GAQ
encode release date: 2022-09-12
lab: Gene Yeo, UCSD
library encode accession: ENCLB383UAZ
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: 701168581

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
All FASTQ passed QC and were aligned to the reference genome GRChg38 using STAR 2.7.9a. BAM files were converted to a raw count expression matrix using HTSeq-count
Assembly: GRChg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: B.fo.IL6.Sp_1

value: Peritoneal Cavity

tag: treatment


title: snRNA-seq from heart (ENCLB895XTF)

description:
https://www.encodeproject.org/experiments/ENCSR252RYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR252RYC
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2024-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB895XTF
size range: 300-600

source_name: Homo sapiens female embryo (115 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: tissue

tag: note

value: Homo sapiens heart tissue

value: embryonic

value: 115 day

value: Michael Snyder, Stanford

value: nucleus

tag: source

value: BDRL

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS282BRL at ENCODE; https://www.encodeproject.org/ENCBS282BRL/


title: eCLIP from K562 (ENCLB340DAE)

description:
https://www.encodeproject.org/experiments/ENCSR004VIR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against EEF2
experiment encode accession: ENCSR004VIR
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR344GAQ
encode release date: 2022-09-12
lab: Gene Yeo, UCSD
library encode accession: ENCLB340DAE
fragmentation methods: see document
size range: 175-300

tag: antibody

value: cell line

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

value: ATCC

tag: link

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: snRNA-seq from heart left ventricle (ENCLB338QDU)

description:
https://www.encodeproject.org/experiments/ENCSR237HWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237HWJ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB338QDU
size range: 300-600

source_name: Homo sapiens male adult (64 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: Sex

value: male

tag: dev stage

value: 64 year

tag: lab

value: Shin Lin

value: nonischemic -> giant cell vs. sarcoid (EF 18%, LVEDD 5.9, LVPWd 0.65)

value: ENCBS667KWK at ENCODE; https://www.encodeproject.org/ENCBS667KWK/

value: Derived from ENCODE donor ENCDO446FXE; https://www.encodeproject.org/ENCDO446FXE/


title: 701168571

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: B.fo.IL1b.Sp_3

value: Peritoneal Cavity

tag: cell type

tag: strain


title: snRNA-seq from heart left ventricle (ENCLB398IAZ)

description:
https://www.encodeproject.org/experiments/ENCSR231FNL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR231FNL
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB398IAZ
size range: 300-600

source_name: Homo sapiens male adult (32 years) heart left ventricle tissue, preserved by flash-freezing

tag: description

value: adult

tag: age

value: 32 year

value: Michael Snyder, Stanford

tag: health state

value: healthy

value: ENCBS684NAD at ENCODE; https://www.encodeproject.org/ENCBS684NAD/

value: Derived from ENCODE donor ENCDO212WIV; https://www.encodeproject.org/ENCDO212WIV/


title: B.fo.IL1b.Sp_2

tag: treatment


title: snRNA-seq from heart (ENCLB847VJF)

description:
https://www.encodeproject.org/experiments/ENCSR644VVE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR644VVE
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB847VJF
fragmentation methods: none
size range: 300-800

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue nuclear fraction

value: heart

value: tissue

value: Encode B6CastF1 2 months male #2 Heart

value: not collected

value: 2 month

value: Barbara Wold, Caltech

tag: subcellular fraction term name

value: nucleus

tag: source

value: The Jackson Laboratory

value: ENCBS166CVE at ENCODE; https://www.encodeproject.org/ENCBS166CVE/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: 701168561

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood