title: CRLM17

city: Beijing

first: Yedan

last: Liu

address: Yiheyuan

institute: Peking University

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level and to identify TCR sequences.
For Smart-seq2 data, HTSeqGenie pipeline (R package version 4.8) was used to quantify gene expression level.
Genome_build: GRCh38 for RNA expression and TCR data.
Supplementary_files_format_and_content: expression matrix (UMI counts), cell metadata, TCR summary.

molecule: polyA RNA

extract_protocol:
Single CD45+ cells (anti-human CD45, HI30, eBiocience) of the samples of each patient were sorted into 1.5 mL low binding tubes (Eppendorf) with 50 μL sorting buffer for droplet-based scRNA-seq, or into wells of 96-well plates (Axygen) for plated-based scRNA-seq, prepared with lysis buffer which contained 1 mL 10 mM dNTP mix (Fermentas), 1 mL 10 mM Oligo dT primer, 1.9 mL 1% Triton X-100 (Sigma) plus 0.1 mL 40 U/ml RNase Inhibitor (Takara). The sealed plates were stored frozen at 80 C.
Fresh tumor, adjacent liver tissue and lymph node samples were cut into approximately 1 mm3 pieces in the RPMI-1640 medium (Invitrogen) with 10% fetal bovine serum (FBS; Sciencell), and enzymatically digested with MACS tumor dissociation kit (Miltenyi Biotec) for 30 min on a rotor at 37 C, according to the manufacturer’s instructions. After filtered by 70 mm Cell-Strainer (BD) in the RPMI-1640 medium (Invitrogen), the suspended cells were centrifuged at 400 g for 5 min. After removing the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Solarbio) and incubated on ice for 2 min to lyse red blood cells. The cell pellets were resuspended in sorting buffer (PBS supplemented with 2% FBS) after washing twice with PBS (Invitrogen). Peripheral blood mononuclear cells (PBMCs) and ascites were isolated using the HISTOPAQUE-1077 (Sigma-Aldrich) solution as previously described51. Briefly, 5 mL fresh peripheral blood or ascites was collected prior to surgery in EDTA anticoagulant tubes and subsequently layered onto HISTOPAQUE-1077. After centrifugation, immune cells remained at the plasma-HISTOPAQUE-1077 interface and were transferred to a new tube, with twice washing using PBS. These immune cells were resuspended with sorting buffers.
10x Chromium Single cell 3’, 10x Chromium Single cell 5’ + VDJ Library, and Smart-seq2 Library

tag: subject status

value: colorectal cancer patients with liver metastasis

value: tumor, adjacent-normal,blood,lymph node

tag: platform


title: CRLM15

status: Public on Feb 12 2022

type: SRA

country: China

library_source: transcriptomic

organism: Homo sapiens

source_name: Single CD45+ cells (anti-human CD45, HI30, eBiocience)

tag: tissue


title: CRLM14


title: Genomic DNA from AYA-49

type: genomic

city: Hong Kong

first: Kay Ka-Wai

last: Li

address: 5/F, Cancer Centre, Prince of Wales Hospital

country: Hong Kong

institute: The Chinese University of Hong Kong

description: glioblastoma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC BeadChip array

scan_protocol: standard recommended Illumina scanner

data_processing:
Bioconductor (Version 3.9) package minifi (Version 1.32.0) using function 'preprocessIllumina'
Matrix.Processed.txt contains Average Beta values
Matrix.Signal.Intensities.txt contains Unmethylated and methylated signal intensities

molecule: genomic DNA

source_name: IDH-wildtype, H3-wildtype glioblastomas of adolescents and young adults

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: Male

tag: age

tag: origin

value: brain

tag: location

value: hemisphere


title: Genomic DNA from AYA-50

description: glioblastoma


title: Genomic DNA from AYA-48

description: glioblastoma


title: Genomic DNA from AYA-47

description: glioblastoma


title: CRLM16


title: Oligodendrocytes Ninj2-deficient rep2 [M_2]

city: Xiamen

first: yuxia

last: sun

address: Xiang'an South Road

institute: Xiamen University

data_processing:
All RNA-Seq data were aligned to mm10 by Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 and StringTie(v1.3.3b) were used to generate gene counts.
Differential expressed genes were identified using DESeq2 with fold change>2.0 and p<0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Oligodendrocytes Ninj2-deficient

growth_protocol: Mouse oligodendrocytes were isolated from the cortices of pups at postnatal day 3 to 8. Briefly, cortical tissues were dispersed into single cells and the cell suspension was then subjected to immunopanning with antibodies against GalC and O4 sequentially. The enriched Galc-negative O4-positive OPCs were plated into PDL-coated culture dishes and culture with mouse oligodendrocydes growth medium.

extract_protocol:
The oligodendrocytes were harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

tag: cell type

value: Primary culture mouse oligodendrocytes

tag: developmental stage

value: differentiation day2


title: Double Positive thymocytes scRNA-seq

city: Frankfurt am Main

first: Adrien

last: Jolly

state: Hessen

address: Theodor Stern Kai 7

country: Germany

institute: University Hospital Frankfurt

data_processing:
data was processed using CellRanger 3.01
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger Output  (raw gene counts matrices)

source_name: thymus

extract_protocol:
Double Positive thymocytes (CD4+CD8+) from a 12 weeks old C57B6-CD45.1/J mouse were sorted (BDFACSAriaIII, 100 μm nozzle) into 500 μl PBS containing 50% FCS. The sorted cells (1364 – 5623 cells per sample)  were spun down at 300 g for 5 mins at 4 C and resuspended in 35 μl FACS buffer. Single cells were captured using the Chromium System and single cell full transcriptome library was generated
Chromium Next GEM Single Cell V(D)J reagents Kits v1.1

treatment_protocol: no treatment

value: Double Positive thymocytes (CD4+CD8+)

tag: strain

tag: treatment

value: untreated


title: Genomic DNA from AYA-46

description: glioblastoma

value: Female


title: small extracellular vesicles derived from white adipose tissue_rep1

type: RNA

city: Chengdu

first: Pengyu

last: Hong

address: No.14, Section 3, Renmin South Road

institute: West China School of Stomatology, Sichuan University

description: Total RNA from sEV-WAT and sEV-BAT was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Then, the RNA expression profiling was performed using Arraystar Mouse LncRNA Arrays V4 platform.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C) and data were extracted using Agilent Feature Extraction Software.

data_processing: Quantile normalization and subsequent data processing were performed using Agilent GeneSpring Software GX v12.1.

source_name: white adipose tissue

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each RNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: For isolation of sEV-WAT and sEV-BAT, brown and white adipose tissue were obtained from the interscapular and inguinal region of 6-week-old C57BL/6 male mice, respectively. The fat pads were washed with sterile PBS, then cut into small pieces under aseptic condition. Then the minced tissues were added into the Celstir Spinner Flask (Wheaton, USA) supplemented with 50-100 mL α-MEM (Hyclone), 100 U/mL penicillin, and 100μg/mL streptomycin and cultured with speed at 100 r/min for 2 days. The debris of tissues and cells were removed by centrifugation at 300g for 5 min and at 2000g for 20 min. The supernatants were collected and concentrated by an additional centrifugation in Ultracel-100 membrane (Millipore) at 5000g, 4°C for 30 min. Afterwards, the sEVs in concentrates were pelleted by ultracentrifugation at 110,000g, 4°C for 70 min (13 PA Tube 1.5×9.6 cm, 332901A, HITACHI, Japan; P40ST swing rotor, himac CP 70MX, HITACHI) and washed with PBS at 110,000g, 4°C for 70 min for a second UC run. Finally, the EV-rich pellet was resuspended in 200 μl of PBS.

tag: source

value: 6-8 weeks


title: CRLM13


title: small extracellular vesicles derived from brown adipose tissue_rep1

source_name: brown adipose tissue


title: small extracellular vesicles derived from white adipose tissue_rep3


title: small extracellular vesicles derived from brown adipose tissue_rep3


title: small extracellular vesicles derived from brown adipose tissue_rep2


title: small extracellular vesicles derived from white adipose tissue_rep2


title: CRLM12


title: Genomic DNA from AYA-44

description: glioblastoma


title: Genomic DNA from AYA-45

description: glioblastoma


title: CRLM10


title: Genomic DNA from AYA-40

description: glioblastoma


title: Genomic DNA from AYA-42

description: glioblastoma


title: Genomic DNA from AYA-43

description: glioblastoma


title: Genomic DNA from AYA-39

description: glioblastoma

value: non-hemisphere


title: Genomic DNA from AYA-37

description: glioblastoma


title: Genomic DNA from AYA-36

description: glioblastoma


title: Genomic DNA from AYA-38

description: glioblastoma


title: CRLM08


title: Oligodendrocytes WT rep1 [C_1]

source_name: Oligodendrocytes WT

value: wild type


title: Genomic DNA from AYA-35

description: glioblastoma


title: Genomic DNA from AYA-41

description: glioblastoma


title: CRLM09


title: D7_GKO_REP1 [SAMPLE 3]

status: Public on Feb 13 2022

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

country: USA

institute: Stanford University

hyb_protocol: Samples were hybridized to an Illumina Methylation EPIC array.

scan_protocol: Samples were read on an iScan.

data_processing: Methylation array .idat files were read using Minfi v1.40.0, and any low-quality probes (detection p-value <0.01) were discarded. Data was swan normalized prior to calculation of M and Beta values. Common CpG SNPs were removed using the dropLociWithSnp command. To extract Differentially Methylated Probes (DMPs), Limma v3.50.0 was used to create a normalized count matrix of M values designed on cell type. Limma estimated the fold changes and standard errors by fitting a linear model for each gene, followed by Empirical Bayes smoothing. Differentially Methylated Regions (DMRs) were determined using the Minfi dmrcate function. DMPs and DMRs were annotated with the Illumina MethylationEPIC annotation file (https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38). Volcano plots were generated using ggplot2 in R.

label: Cy5 and Cy3

label_protocol: Bisulfite conversion was performed using the EZ DNA Methylation kit (Zymo), followed by Illumina Methylation EPIC array for Genotyping.

growth_protocol: Human embryonic stem cells (H9, female) were maintained in E8 medium (Life Technologies) on Matrigel (Stem Cell Technologies) coated plates, dissociated using 0.5mM EDTA, and passaged at 1:10 ratio.

extract_protocol: Cells were collected using Accutase. DNA was isolated from cells using the Qiagen DNA Blood and Tissue Kit.

treatment_protocol: For differentiations, the media was changed to Essential 6 (Life Technologies) supplemented with 1μM retinoic acid (Sigma) and 5 ng/mL Recombinant Human BMP4 (R&D Systems), and replaced every two days for seven days. On day 7, cells were collected for downstream analysis.

value: hESCs

tag: genotype

value: GKO


title: CRLM06


title: Oligodendrocytes Ninj2-deficient rep1 [M_1]


title: HESC_WT_REP2 [SAMPLE 6]

description: hESC

source_name: hESC

value: WT


title: Oligodendrocytes WT rep2 [C_2]


title: HESC_GKO_REP2 [SAMPLE 8]

description: hESC


title: CRLM11


title: Genomic DNA from AYA-32

description: glioblastoma


title: Genomic DNA from AYA-31

description: glioblastoma


title: Genomic DNA from AYA-29

description: glioblastoma


title: CRLM05


title: CRLM04


title: HESC_WT_REP1 [SAMPLE 5]

description: hESC


title: Genomic DNA from AYA-27

description: glioblastoma


title: Genomic DNA from AYA-30

description: glioblastoma


title: CRLM03


title: Genomic DNA from AYA-26

description: glioblastoma


title: CRLM02


title: D7_GKO_REP2 [SAMPLE 4]


title: Genomic DNA from AYA-23

description: glioblastoma


title: Genomic DNA from AYA-24

description: glioblastoma


title: Genomic DNA from AYA-28

description: glioblastoma


title: Genomic DNA from AYA-21

description: glioblastoma


title: Genomic DNA from AYA-22

description: glioblastoma


title: mESC_CTCFAID_ChIP_input_24h_r2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: ChIP input DNA in E14TG2a mESCs (with OsTir1; CTCF-AID-eGFP), after 24h of IAA

library_source: genomic

data_processing:
DamID: The full protocol is described in the corresponding manuscript. The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17. Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. LADs were called using hidden Markov modeling (https://github.com/ gui11aume/HMMt). Additionally, individual replicates were averaged for create a combined data track and LAD model.
ChIP-seq: The full protocol is described in the corresponding manuscript. Reads were mapped to a concatenated reference genome (mm10 and hg19) using bowtie2 2.3.4.1. Reads were filtered for a mapping quality of at least 15 and optical PCR duplicates were removed with SAMtools 1.9. Deeptools 3.0 was used to create a normalized coverage track, scaled to 1 million HEK293T reads. Peak calling was performed with MACS2 2.1.1.20160309 at a q-value cutoff of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: DamID: BigWig files of log2-normalized LaminB1 pADamID scores for 10kb genomic bins, bed file with LAD coordinates; ChIP-seq: BigWig file of coverage, bed file with peak coordinates.

growth_protocol: Mouse neural precursor cells (mNPCs) were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), recombinant mouse EGF (10 ng/ml; PeproTech) and recombinant human FGF-basic (10 ng/ml; PeproTech) on 0.1% gelatin-coated plates. Cells were passaged every 3-4 days. E14Tg2a mouse embryonic stem cells (mESCs) and derived cell lines were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), 104 U of leukemia inhibitory factor (LIF; Millipore), the MEK inhibitor PD0325901 (1 μM; Selleckchem), the GSK-3β inhibitor CHIR99021 (3 μM; Cayman Chemical) and 1-thioglycerol (1.5 × 10−4 M; Sigma-Aldrich) on 0.1% gelatin-coated plates. The cell lines were passaged every two days.

extract_protocol:
DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit. The DNA concentration was estimated with a Nanodrop; ChIP-seq: ChIP experiments were performed in the presence of 10% human HEK293T cells as internal reference. Cells were crosslinked (1% FA, 10 minutes) and quenced with glycine (2.0M). Chromatin was fragmented to ~300 bp fragments with a Bioruptor Plus sonication device (Diagenode). CTCF antibody (07-729, Merck Millipore; 5 μL per ChIP) was coupled with Protein G beads (Thermo Fisher Scientific) and incubated with fragmented chromatin overnight at 4 °C. Released DNA fragments were purified with the MinElute PCR Purification kit (Qiagen).
DamID: The full protocol is described in Leemans, 2019. 500 ng of genomic DNA was digested with DpnI at Dam-methylated GATC sequences, and ligated to adapters. Subsequent DpnII digestion destroyed DNA fragments containing unmethylated GATC sequences. DNA fragments were then amplified with 15-22 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; ChIP-seq: The purified DNA fragments were prepared with the KAPA HTP Library Preparation kit (Roche).
mNPC samples: Illumina HiSeq 2500, 65 bps single-end; mESC samples: Illumina NextSeq, 75 bps single-end

treatment_protocol: DamID: Cells were transduced with lentiviral particles containing either Dam-control or Dam-LaminB1 constructs and cultured for an additional 3 days; ChIP-seq: Protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich).

value: Embyonic stem cell

tag: protocol

value: ChIP-seq

tag: genetic modification

value: OsTir1; CTCF-AID-eGFP

tag: time point


title: Genomic DNA from AYA-20

description: glioblastoma


title: Genomic DNA from AYA-25

description: glioblastoma

value: Male


title: CRLM07

tag: subject status

value: colorectal cancer patients with liver metastasis

value: tumor, adjacent-normal,blood,lymph node

tag: platform


title: Genomic DNA from AYA-18

description: glioblastoma

tag: Sex

value: brain

value: hemisphere


title: Genomic DNA from AYA-17

description: glioblastoma

tag: age


title: mESC_CTCFAID_ChIP_input_24h_r1


title: mESC_CTCFAID_ChIP_input_0h_r2

description: ChIP input DNA in E14TG2a mESCs (with OsTir1; CTCF-AID-eGFP), after 0h of IAA


title: Genomic DNA from AYA-16

description: glioblastoma

tag: origin


title: HESC_GKO_REP2 [SAMPLE 7]

description: hESC


title: Genomic DNA from AYA-15

description: glioblastoma

tag: location


title: D7_WT_REP2 [SAMPLE 2]


title: mESC_CTCFAID_ChIP_input_0h_r1


title: Genomic DNA from AYA-11

description: glioblastoma


title: Genomic DNA from AYA-13

description: glioblastoma


title: Genomic DNA from AYA-14

description: glioblastoma


title: Genomic DNA from AYA-19

description: glioblastoma


title: Genomic DNA from AYA-10

description: glioblastoma


title: mESC_CTCFAID_ChIP_H3K27me3_24h_r1

description: H3K27me3 ChIP-seq in E14TG2a mESCs (with OsTir1; CTCF-AID-eGFP), after 24h of IAA

tag: antibody


title: Genomic DNA from AYA-12

description: glioblastoma


title: Genomic DNA from AYA-7

description: glioblastoma


title: Genomic DNA from AYA-9

description: glioblastoma


title: mESC_CTCFAID_ChIP_H3K27me3_0h_r2

description: H3K27me3 ChIP-seq in E14TG2a mESCs (with OsTir1; CTCF-AID-eGFP), after 0h of IAA


title: Genomic DNA from AYA-8

description: glioblastoma


title: CRLM01

tag: tissue


title: Genomic DNA from AYA-6

description: glioblastoma


title: Genomic DNA from AYA-4

description: glioblastoma


title: SC200

city: PITTSBURGH

first: TORU

last: NYUNOYA

state: PA

address: NW628 UPMC MONTEFIORE, 3459 FIFTH AVENUE

institute: UNIVERSITY OF PITTSBURGH

description:
SC200_S1_L00*
whole lung tissue, single cell suspension

data_processing:
10X Genomics' Cell Ranger 3 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 3 software's cellranger count function
Cell Ranger output of raw_gene_bc_matrices were utilized for further downstream analysis in R with the package Seurat v3, only cells expressing at least 200 genes were kept for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files contain gene UMI counts per cell for each sample

source_name: whole lung

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide

tag: disease

value: COPD

value: Lung


title: D7_WT_REP1 [SAMPLE 1]

tag: cell type


title: mESC_CTCFAID_ChIP_H3K27me3_0h_r1

extract_protocol:
DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit. The DNA concentration was estimated with a Nanodrop; ChIP-seq: ChIP experiments were performed in the presence of 10% human HEK293T cells as internal reference. Cells were crosslinked (1% FA, 10 minutes) and quenced with glycine (2.0M). Chromatin was fragmented to ~300 bp fragments with a Bioruptor Plus sonication device (Diagenode). CTCF antibody (07-729, Merck Millipore; 5 μL per ChIP) or H3K27me3 antibody (PAB-195-050, Diagenode) was coupled with Protein G beads (Thermo Fisher Scientific) and incubated with fragmented chromatin overnight at 4 °C. Released DNA fragments were purified with the MinElute PCR Purification kit (Qiagen).
DamID: The full protocol is described in Leemans, 2019. 500 ng of genomic DNA was digested with DpnI at Dam-methylated GATC sequences, and ligated to adapters. Subsequent DpnII digestion destroyed DNA fragments containing unmethylated GATC sequences. DNA fragments were then amplified with 15-22 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; ChIP-seq: The purified DNA fragments were prepared with the KAPA HTP Library Preparation kit (Roche).
mNPC samples: Illumina HiSeq 2500, 65 bps single-end; mESC samples: Illumina NextSeq, 75 bps single-end


title: SC170

description:
SC170_S2_L00*
whole lung tissue, single cell suspension


title: SC167

description:
SC167_S1_L00*
whole lung tissue, single cell suspension


title: Genomic DNA from AYA-3

description: glioblastoma

value: Female


title: MCF-7 siRBCK1_1

city: Xinxiang

first: ning

middle: jia

last: fan

state: Henan

address: Xinxiang Medical College

institute: Xinxiang Medical College

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include FPKM values for each Sample

source_name: human breast cancer cell line MCF-7

growth_protocol: MCF7 cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: MCF-7 cells were transfected with siControl or siRBCK1.

value: breast

tag: cell line

tag: disease state

value: breast cancer

tag: transfection


title: MCF-7 siRBCK1_2


title: Genomic DNA from AYA-2

description: glioblastoma


title: MCF-7 siControl_3

value: siControl


title: MCF-7 siControl_2


title: MCF-7 siControl_1


title: luc_ChIRPseq_rep3

city: Frederiksberg C

first: Yu

last: Jin

address: Thorvaldsensvej 40, 2nd floor

country: Denmark

institute: University of Copenhagen

data_processing:
library strategy: ChIRP-Seq
Illumina Casava1.7 software used for basecalling.
adapter was trimmed by Trim Galore v0.6.7 in paired-end mode and then aligned to TAIR10 by STAR v2.7.8a [58] in local mode. Aligned reads with MAPQ below 10 were removed by Samtools v1.1.2 [59]. BAM files were converted to unstranded Bedgraph files using BEDtools genomecov v2.30.0 [55]. The code was detailed in the section FLAIL_2021, RNA-seq.sh in the mentioned GitHub page. Differentially expressed gene(s) (DEGs) were estimated based on the number of reads mapped against unique locus using the DESeq2 tool [60]. Data were log 2 transformed to identify the genes with significant differential expression with a criteria of fold change, |log2 fold change| > 1 and P value < 0.05. GO enrichment was analyzed by Metascape [38].
Align to TAIR10 using STAR v2.7.8a in local mode
Filter out MAPQ reads below 5 and remove PCR duplicates by Samtools v1.1.2
Convert BAM files to Bedgraph using BEDtools genomecov v2.30.0; Convert BAM files to BigWig using bamCoverage 3.5.1
calling peaks by CCAT3.0
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files show sequencing coverage with single base resolution (no signal smoothing, transformation or normalization were applied)

organism: Arabidopsis thaliana

source_name: Whole seedlings

extract_protocol:
The antisense oligonucleotide probes Even and Odd were designed against the full-length FLAIL sequence, The probes were biotinylated at 3′ end. Antisense oligonucleotides targeting luciferase RNA were used as negative control. Crosslinked seedlings (2.5 g) were ground and suspended in 10 ml Honda Buffer. After RNA immunoprecipitation, DNA was extracted using ChIP DNA Clean & Concentrator (Zymo Research) and used for subsequent DNA sequencing.
ChIRP-seq libraries were constructed using the ChIP-seq Library Prep Kit (NOVA-5143-02 with NEXTflex® ChIP-seq Barcodes-24) following the manufacturer's protocol and quantified on Agilent 2100 Bio-analyzer.  ChIRP-seq libraries were pooled into one flow cell (NextSeq 500/550 High Output Kit v2.5) for sequencing with single-indexed, PE (2*75 bp) and sequenced on an Illumina Nextseq 500.

value: 14-day seedlings

tag: ecotype

value: Columbia (Col-0)

tag: genotype

value: wild type

tag: treatment

value: untreated


title: Genomic DNA from AYA-5

description: glioblastoma

value: non-hemisphere


title: luc_ChIRPseq_rep2


title: MCF-7 siRBCK1_3


title: luc_ChIRPseq_rep1


title: odd_ChIRPseq_rep2


title: AGS siDUB1_2

first: Zhongbo

last: li

institute: Xinxiang medical university

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

source_name: human gastric cancer cell line AGS

growth_protocol: AGS cells were plated in 12-well plates at 30% fusion per well

treatment_protocol: AGS cells were transfected with siControl or siDUB1.

value: stomach

value: AGS

value: gastric cancer


title: Genomic DNA from AYA-1

description: glioblastoma

value: Male


title: odd_ChIRPseq_rep1


title: Exhausted CD8 T cells rep2

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

hyb_protocol: Microarray microRNA 2.0 (Affymetrix) was performed at the Penn Microarray Facility

scan_protocol: standard Affymetrix protocol

data_processing: Cel files from the Microarrays were read in R using the ReadAffy function from affy package and the counts were quantile normalized using the NormiR function,Expression values normalized using R package limma by fitting the counts data to a model based on groups,from ExiMiR package

label: biotin

source_name: Sorted T cells from chronic LCMV infected mice d30 pi

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol extraction  was performed according to the manufacturer's instructions.

treatment_protocol: Sorted LCMV Db gp-33 specific and naïve CD8 T cells were resuspended in TRIzol (Thermo Fisher Scientific).

value: spleen


title: Exhausted CD8 T cells rep3


title: even_ChIRPseq_rep1


title: Early Exhaustion CD8 T cells rep2

source_name: Sorted T cells from chronic LCMV infected mice d8 pi


title: Early Exhaustion CD8 T cells rep1


title: Exhausted CD8 T cells rep1


title: Early Exhaustion CD8 T cells rep3


title: AGS siControl_1


title: Memory CD8 T cells rep2

source_name: Sorted T cells from acute LCMV infected mice d30 pi


title: Memory CD8 T cells rep3


title: Memory CD8 T cells rep1


title: MUTE GFP IP_rep3

city: Austin

first: Keiko

middle: U

last: Torii

address: 2506 SPEEDWAY

institute: University of Texas at Austin

data_processing:
Output reads were mapped to the TAIR10 genome assembly using bowtie2
resulting bam files were sorted and indexed via samtool
The sorted bam files were subjected for MACS peak calling (version 2.1.0.20140616)
Genome_build: TAIR10
Supplementary_files_format_and_content: txt, peak file

source_name: seedling

growth_protocol: Homozygous transgenic lines for proMUTE::MUTE-GFP scrm-D were grown on ½ MS agar media for 2 days.

extract_protocol:
Purified chromatin was sheared by sonication and GFP-DNA complexes were isolated by anti-GFP antibody
The half of the purified DNA was subjected to library preparation using ACCEL-NGS® 2S PLUS DNA LIBRARY KIT with 2S Set A MID Indexing Kit (Swift bioscience, 21024, 26148) for next generation sequencing. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: 60mg of initial material (seeds) for wild type and each replicate were grown in a ½ MS liquid media, non-treated

value: proMUTE::MUTE-GFP scrm-D

value: 2 day post germination

value: entire seedling

tag: chip antibody


title: AGS siDUB1_3


title: AGS siDUB1_1


title: MUTE input_rep3


title: AGS siControl_3


title: Effector CD8 T cells rep2

source_name: Sorted T cells from acute LCMV infected mice d8 pi


title: AGS siControl_2


title: NonSilkOrganoidD120_1

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich

data_processing:
Basecalling using bcl2fastq 2.19
Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters  and GrCh38 as the reference genome
Seurat (v 4.0.6 and R version 4.1.0) was applied to the scRNA-data for downstream analysis of matrix files.
Genome_build: GrCH38

source_name: Non-silk organoid culture day 120

growth_protocol: To start 3D organoid formation, homogeneous hPSC culture at 75-90% confluency of the well area was washed with DPBS (-/-), Thermo Fisher Scientific, 14200075) and incubated with Accutase solution (50 μL/cm², Thermo Fisher Scientific, A1110501) for 5 min at 37°C. The cells were then centrifuged, resuspended in mTeSR1 (Stem Cell Technologies, 05850) with 10μM Y-27632 and counted. Single cell suspension was then seeded at a density of 8000 cells/well in an ultra-low attachment 96-well plate (Costar, round bottom, REF 7007) and supplemented with mTeSR1 with 10μM Y-27632 to reach a final volume of 250 μL/well as reported in Lancaster et al[12]. After two days of culture, 50% of media was replaced with mTesR1 without the Y-27632 supplement. , Thermo Fisher Scientific, 14200075) and incubated with Accutase solution (50 μL/cm², Thermo Fisher Scientific, A1110501) for 5 min at 37°C. The cells were then centrifuged, resuspended in mTeSR1 (Stem Cell Technologies, 05850) with 10μM Y-27632 and counted. Single cell suspension was then seeded at a density of 8000 cells/well in an ultra-low attachment 96-well plate (Costar, round bottom, REF 7007) and supplemented with mTeSR1 with 10μM Y-27632 to reach a final volume of 250 μL/well as reported in Lancaster et al[12]. After two days of culture, 50% of media was replaced with mTesR1 without the Y-27632 supplement. After three additional days, differentiation medium consisting of DMEM/F12 (Thermo Fisher Scientific, 21331020), 1:100 N2 supplement (Thermo Fisher Scientific, 17502048) and 2 μg/mL Heparin (Sigma-Aldrich, H3149) was added from day 0-6 and replaced every second day. 1% minimum essential medium non-essential amino acids (MEM-NEAA; Sigma-Aldrich, M7145), 0.1% 2-mercaptoethanol (Merck, 8057400005), 1:500 penicillin-streptomycin (Thermo Fisher Scientific, 15140122), and 200 mM L-glutamine (Thermo Fisher Scientific, 25030081) were maintained for the entire differentiation period, as reported in Lancaster et al [12]. For the first 48h the medium was also supplemented with 3% Knockout Serum Replacement (KSR, Thermo Fisher Scientific, 10828010). At day 8 each organoid was transferred in a sterile dimple, embedded evenly in 30uL of matrigel (Corning, 354234) and incubated at 37°C for 25 min. After the polymerisation of matrigel was complete, the organoids were transferred in an ultra-low attachment 6 well plate (Corning, flat bottom, REF 3471) with 4mL/well of 1:1 DMEM/F12:Neurobasal medium (Thermo Fisher Scientific, 21331020 and A3582901), 1:200 N2 supplement, 1:100 B27 supplement (Thermo Fisher Scientific, 12587010) and 2.5 μg/mL insulin (Sigma-Aldrich, I9278-5ML), as reported in Lancaster et al [12]. The medium was replaced every second day. At day 15, the medium was substituted with 1:1 DMEM/F12:Neurobasal, 1:200 N2 supplement, 1:50 B27+Vitamin A supplement (Thermo Fisher Scientific, 17504044) and 2.5 μg/mL Insulin solution supplemented with 400μM Ascorbic Acid (Sigma-Aldrich, A4403-100MG). For terminal differentiation after day 25, the previously described medium was supplemented with 400μM Ascorbic Acid, 10ng/mL BDNF (Miltenyi, 130-096-286), 10ng/mL GDNF (R&D Systems, 212-GD-010) and 200μM cAMP (Sigma-Aldrich, D0627-1G).

extract_protocol:
For 10x Genomics single cell RNA sequencing,  single cell suspensions were loaded onto 10x Genomics Single Cell 3′ Chips along with the mastermix as per the manufacturer’s protocol
According to 10X protocols.

treatment_protocol: Silk organoids: A 20μL droplet of prepared Biosilk solution (BioLamina, BS-0101) functionalized with 5μg/mL Lam-111 (BioLamina, LN111) and 10 μM Y-27632 was placed in the centre of hydrophobic cell culture wells of a 24-well plate (Sarstedt, REF 833922500)[17]. Air bubbles were introduced into the droplets by pipetting up and down (10-15 strokes) creating a dense foam. Human pluripotent stem cells were detached using Accutase solution (50 μL/cm²) and prepared as a single cell suspension at high concentration (15’000 cells/μL in mTeSR1 with 10 μM Y-27632). A total of 75’000 cells was then added to the silk foam, dispersed homogeneously, and stabilized at 37°C for 25 min. Silk bioengineered culture was then incubated with 2mL of mTeSR1 with 10 μM Y-27632 for 5 days and then cultured following the cerebral differentiation protocol as described in Lancaster et al [12]. Eight days after the start of differentiation, silk organoids were lift up with a scalper, detached from the bottom and grown in suspension (free floating) in a 6-well plate (Corning, 3471).

tag: culture condition

value: Non-silk

tag: days in culture


title: SilkOrganoidD120_2

source_name: Silk organoid culture day 120

value: Silk


title: Effector CD8 T cells rep3


title: MUTE GFP IP_rep2


title: mESC_CTCFAID_ChIP_H3K27me3_24h_r2

value: Embyonic stem cell

tag: protocol

value: ChIP-seq

tag: genetic modification

value: OsTir1; CTCF-AID-eGFP

tag: time point


title: SilkOrganoidD120_1


title: MUTE input_rep2

tag: age


title: MUTE GFP IP_rep1


title: Naive CD8 T cells rep3

source_name: Sorted T cells from non infected Mice


title: efae_wt_UT_rep03

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
library strategy: HT-5PSeq
Demultiplexing using bcl2fastq v2.20.0.422 at default settings, allowing one barcode-mismatch and minimum read length of 35nt
Quality control with FASTQC and MultiQC v1.9 tools at default parameters
Adapter trimming using cutadapt 2.3 with Python 3.7.2, options: --minimum-length 28; -e 0.2; -o 9; --nextseq-trim 20, Adapter 1 AGATCGGAAGAGCAC
Extraction of barcodes and UMI using umitools and options --bc-pattern CCCCCCNNNNNNNN
Sequences were mapped using STAR with the options: --alignEndsType Extend5pOfRead1; --outFilterMatchNminOverLread 0.9; --outFilterMultimapNmax 8; --limitBAMsortRAM 100000000000
Deduplication using UMIs was done with umitools
Count statistics on species and RNA composition were determined using bedtools intersect (aka intersectBed) Version: v2.29.2, bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>
Genome_build: NCBI Enterococcus faecalis GCF003319925.1_ASM331992v_genomic.fna and GCF_003319925.1_ASM331992v1_genomic.gff
Supplementary_files_format_and_content: Bedgraphs of forward (fwd) and reverse (rev) 5P read positions were created using BEDTools genomecov program with options {-bg -strand [+/-] -5}  Enterococcus faecalis genome. Only read 1 was used for the analysis.

organism: Enterococcus faecalis

growth_protocol: E. faecalis TX5332 Δlsa::kan was transformed with either the empty vector (pCIEspec) or a vector expressing poxTA (pCIEspec:poxtA-EF9F6) (which should confer Linezolid resistance). 50 ml cultures were inoculated from an overnight culture to OD600=0.005,  grown in filtered BHI media at 37 °C in the presence of 100 ng/ml cCF10 peptide to induce poxtA expression, and were treated with 4 ug/ml Linezolid at OD 600 0.3 for 10 mins, before harvest via centrifugation.

extract_protocol:
RNA was extracted via phenol-chlorofrom extraction, briefly; 300 ul LET-phenol was added to cell pellets and vortexed with an equal volume of 0.1 mm glass beads to lyse cells. 250 ul of water and 250 ul of acidic phenol/chlorophorm was added before votexing  for a further 2 minutes. RNA was then extracted from the aqueous phase with an acidic phenol/chloraform and chloroform extraction step and ethanol precipitated in the presence of NaOAc pH 5.2. RNA was assessed by running a 2 % agarose gel and quantified by Qubit.
HT-5PSeq libraries were prepared as described in (Zhang and Pelechano, Cell Reports Methods, Volume 1, Issue 1,2021). Briefly, 4µg total RNA, total RNA from Enterococcus faecalis was used and ligated over night at 16˚C to r5P_RNA_ oligo (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rNrNrNrNrNrNrNrN) and subsequent purified using 1.8x volumes of RNAClean XP beads (Beckman Coulter). Ligated RNA was then reverse transcribed using random hexamer  (5Pseq-RT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN, 20µM) to prime. Left over RNA was degraded using NaOH. Ribosomal RNA was removed using previously described rRNA DNA oligo depletion mixes (Huch, Nersisyan et al doi: https://doi.org/10.1101/2021.04.08.439066), following duplex-specific nuclease (DSN, Evrogen) degradation. rRNA depleted cDNA was amplified by PCR (17 cycles) and enriched for fragments with the range of 300-500nt using Ampure XP. Size selected HT-5P Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequenced using a NextSeq2000 Illumina sequencer (100cycles P3 kit).

treatment_protocol: 4 ug/ml Linezolid for 10 mins

tag: strain information

value: E. faecalis TX5332 {delta}lsaA (lsa::Kan)/pCIEspec

tag: culture conditions

value: BHI exponential growth

tag: library protocol


title: Effector CD8 T cells rep1

source_name: Sorted T cells from acute LCMV infected mice d8 post infection

tag: tissue


title: efae_wt_UT_rep02


title: XG rep 3

city: Amherst

first: Peter

last: Chien

state: MA

address: 240 Thatcher Rd, Life Science Laboratories Room N325

department: Biochemistry and Molecular Biology

institute: University of Massachusetts Amherst

data_processing:
Illumina software used for base-calling and trimming
Burrows Wheeler Alignment (BWA) used to map the reads to Caulobacter Crescentus genome and sorted with SAMtools
Aligned (.bam) files mapped using bedtools map
Genome_build: NC_011916
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caulobacter vibrioides NA1000

source_name: delta lon clpX* strain

growth_protocol: Strains were grown at 30 degrees celsius in liquid peptone yeast extract (PYE)

extract_protocol:
RNA was extracted using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: delta lon clpX*


title: Naive CD8 T cells rep2


title: R_seroneurons_3

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Low quality ends and adapter removal/trimming were performed using cutadapt. Trimmed reads were mapped using STAR30 and assigned to genes with featurecounts31, and normalized counts and differential expression and statistics were calculated using the DESeq2 R package32
Genome_build: hg19

source_name: iPSC-derived neurons

growth_protocol: The growth protocols have been described in our study (Vadodaria et al)- serotonergic neurons were derived from patient iPSCs. In vitro derivation of neurons from human iPSC with using a modified version of a protocol by Lu et al.

extract_protocol:
RNA was extracted with trizol and phenol chloroform precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatments were performed

tag: cell type

value: Serotonergic neurons

value: iPSC-derived neurons

value: adult

tag: disease state

value: major depressive disorder (MDD) patient SSRI remitter


title: efae_wt_LZD_rep03

value: BHI exponential growth 4 ug/ml Linezolid for 10 mins


title: MUTE input_rep1


title: Naive CD8 T cells rep1

value: spleen


title: Genomic DNA from AYA-34

description: glioblastoma

source_name: IDH-wildtype, H3-wildtype glioblastomas of adolescents and young adults

tag: Sex

value: Male

tag: origin

value: brain

tag: location

value: hemisphere


title: Genomic DNA from AYA-33

description: glioblastoma

value: Female


title: efae_wt_UT_rep01


title: XG rep 2


title: R_seroneurons_2


title: efae_wt_LZD_rep02


title: MCF-7 cells, knockdown of ts-ARFGEF1, rep2

city: Taipei

first: Trees-Juen

last: Chuang

address: 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academic Sinica

description: Gene expression data from knockdown of ts-ARFGEF1

hyb_protocol: Total RNA was hybridized to Affymetrix Human Clariom D Assay (transcript (gene) version,Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanncer 3000 7G

data_processing: The microarray raw data was analyzed using Transcriptome Analysis Console (TAC 4.0) software (Affymetrix).

source_name: MCF-7 cells, knockdown of ts-ARFGEF1

label_protocol: Standard Affymetrix protocol.

growth_protocol: MCF-7 cells were culture in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin at 37oC and placed in a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA from cells were extracted using TRIzol reagent with PureLink RNA Mini Kit (Ambion) and PureLink DNase Set (Ambion).

treatment_protocol: MCF-7 were seeded into 6 well plates and transfected with LNA modified antisense oligos (ASO, 10 nM) against NCL junction of ts-ARFGEF1 using TransIT-X2 reagent (Mirus)

tag: cell line

tag: genotype

value: ts-ARFGEF1 knockdown


title: MCF-7 cells, knockdown of ts-ARFGEF1, rep1


title: MCF-7 cells, knockdown of ts-ARFGEF1, rep3


title: R_seroneurons_1


title: efae_wt_LZD_rep01


title: DL rep 3

source_name: delta lon strain

value: delta lon


title: VPA-oxytocin-rep3

city: Honjo, Chuo-ku, Kumamoto

first: Kazuya

last: Matsuo

department: IMEG

country: Japan

institute: Kumamoto University

hyb_protocol: After fragmentation, cDNA (5.5 µg) were hybridized for 17 hr at 45℃ on Affymetrix Rat Gene 2.0 ST Array. GeneChips were stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into the Affymetrix Expression Console™ Software and CHP files were generated.

organism: Rattus norvegicus

source_name: Brain

label_protocol: Biotinylated sense-strand DNA targets were prepared from expressed transcripts (100 ng total RNA) using Ambion WT Expression Kit and GeneChip WT Terminal Labeling and Controls Kit (Affymetrix).

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene).

value: Sprague-Dawley

tag: gender

value: male

value: 8 weeks

value: dorsal hippocampus

tag: prenatal exposure

value: Valproic acid (VPA)

tag: treatment

value: Oxytocin


title: VPA-oxytocin-rep2


title: DL rep 1


title: DL rep 2


title: efae_poxTA_UT_rep03

value: E. faecalis TX5332 {delta}lsaA (lsa::Kan)/pCIEspec:poxtA-EF9F6

value: BHI exponential growth


title: NR_seroneurons_1

value: Serotonergic neurons

value: iPSC-derived neurons

value: adult

value: major depressive disorder (MDD) patient SSRI nonremitter


title: WT rep 3

source_name: wild-type strain

value: wild-type


title: H_seroneurons_3

value: neurotypical healthy control


title: efae_poxTA_UT_rep01


title: efae_poxTA_LZD_rep03

value: BHI exponential growth 4 ug/ml Linezolid for 10 mins


title: VPA-oxytocin-rep1


title: NR_seroneurons_3


title: XG rep 1

value: delta lon clpX*


title: VPA-vehicle-rep3

value: Vehicle


title: VPA-vehicle-rep1

value: Sprague-Dawley


title: MCF-7 cells, negative control for knockdown of ts-ARFGEF1, rep3

description: Gene expression data from negative control for knockdown of ts-ARFGEF1

value: control


title: H_seroneurons_2


title: efae_poxTA_LZD_rep02


title: MCF-7 cells, negative control for knockdown of ts-ARFGEF1, rep2


title: WT rep 2


title: H_seroneurons_1


title: WT rep 1


title: MCF-7 cells, negative control for knockdown of ts-ARFGEF1, rep1


title: efae_poxTA_UT_rep02


title: efae_poxTA_LZD_rep01


title: VPA-vehicle-rep2

value: male

value: 8 weeks


title: Control-vehicle-rep2

value: dorsal hippocampus

value: Control


title: SomMuscle_P9H8

status: Public on Feb 11 2022

city: Heidelberg

first: Jessica

last: Velten

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

institute: University of Heidelberg

data_processing:
Adapter trimming, perl
Pseudoalignment, kallisto 0.43.0
Count tables, R 3.5.1/scater 1.10.1
Genome_build: Drosophila melanogaster, BDGP6 ensemble
Supplementary_files_format_and_content: Kallisto output (tsv)

organism: Drosophila melanogaster

source_name: Somatic muscle

extract_protocol:
Collections of 19-20h old Drosophila embryos were collected and dissociated. Cells were stained with Dapi and DRAQ5 to exclude debris. Single cells were sorted into 96-well-plates in Smart-seq2 lysis buffer. Full-length cDNA from individual cells were produced following the SmartSeq2 protocol.
Smart-Seq2 (modified from Picelli et al., Nature Protocols 2014) Tagmentation using Homemade Tn5 (Hennig et al., G3 2018)

tag: population

value: Mhc-GFP+ DAPI- DRAQ5+


title: SomMuscle_P9H5


title: SomMuscle_P9H10


title: SomMuscle_P9H6


title: Skin_biopsy_CCLE, case4

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: 6yo_spayedFemale_WestHighlandWhiteTerrier

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler.

scan_protocol: Cartridges were run on a Nanostring Sprint machine.

data_processing: Data were analyzed with nSolver software version 4.0.

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol.

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNeasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: Chronic Cutaneous Lupus Erythematosus with hypoadrenocorticism (Addison's-like disease) and secondary pyoderma


title: Control-vehicle-rep1

tag: age


title: SomMuscle_P9H4


title: Skin_biopsy_CCLE, case3

value: Chronic Cutaneous Lupus Erythematosus with hypoadrenocorticism (Addison's-like disease)


title: Skin_biopsy_CCLE, case2

value: Chronic Cutaneous Lupus Erythematosus with suspected Systemic Lupus Erythematosus


title: Skin_biopsy_CCLE, case1


title: SomMuscle_P9H3


title: SomMuscle_P9G9


title: SomMuscle_P9G11


title: SomMuscle_P9G7


title: SomMuscle_P9F9


title: SomMuscle_P9F5


title: SomMuscle_P9F6


title: SomMuscle_P9G1


title: SomMuscle_P9G3


title: SomMuscle_P9G6


title: SomMuscle_P9F3


title: SomMuscle_P9F8


title: even_ChIRPseq_rep2

source_name: Whole seedlings

value: 14-day seedlings

tag: ecotype

value: Columbia (Col-0)

value: wild type

value: untreated


title: SomMuscle_P9F2


title: SomMuscle_P9E5


title: SomMuscle_P9E7


title: SomMuscle_P9H7


title: SomMuscle_P9D2


title: SomMuscle_P9D9


title: SomMuscle_P9D5


title: SomMuscle_P9C8


title: SomMuscle_P9C7


title: SomMuscle_P9D1


title: SomMuscle_P9C10


title: SomMuscle_P9D10


title: SomMuscle_P9C4


title: SomMuscle_P9C9


title: SomMuscle_P9C6


title: SomMuscle_P9C2


title: SomMuscle_P9B11


title: SomMuscle_P9B7


title: SomMuscle_P9A9


title: SomMuscle_P9B2


title: SomMuscle_P8H12


title: SomMuscle_P9E2


title: SomMuscle_P9A5


title: SomMuscle_P8H4


title: SomMuscle_P8H8


title: SomMuscle_P9A8


title: NR_seroneurons_2

value: Serotonergic neurons

value: iPSC-derived neurons

value: adult

value: major depressive disorder (MDD) patient SSRI nonremitter


title: SomMuscle_P8G12


title: SomMuscle_P8G11


title: SomMuscle_P8G9


title: SomMuscle_P8H1


title: SomMuscle_P8H2


title: SomMuscle_P8G7


title: SomMuscle_P8G6


title: SomMuscle_P9B10


title: SomMuscle_P8G3


title: SomMuscle_P8G4


title: SomMuscle_P8G1


title: SomMuscle_P8F9


title: SomMuscle_P8H11


title: SomMuscle_P8F11


title: SomMuscle_P8F6


title: SomMuscle_P8F4


title: SomMuscle_P8H10


title: SomMuscle_P8F3


title: SomMuscle_P8F2


title: SomMuscle_P8E12


title: SomMuscle_P8E10


title: SomMuscle_P8E11


title: SomMuscle_P8E8


title: SomMuscle_P8E6


title: SomMuscle_P8E5


title: SomMuscle_P8G5


title: SomMuscle_P8E4


title: SomMuscle_P8G2


title: SomMuscle_P8D11


title: SomMuscle_P8D9


title: SomMuscle_P8D5


title: SomMuscle_P8D12


title: SomMuscle_P8D3


title: SomMuscle_P8C12


title: SomMuscle_P8F7


title: SomMuscle_P8E7


title: SomMuscle_P8D2


title: SomMuscle_P8C6


title: SomMuscle_P8D1


title: SomMuscle_P8C8


title: SomMuscle_P8C5


title: SomMuscle_P8C1


title: SomMuscle_P8C4


title: SomMuscle_P8B11


title: SomMuscle_P8B9


title: SomMuscle_P8C3


title: SomMuscle_P8B10


title: SomMuscle_P8E1


title: SomMuscle_P8B6


title: SomMuscle_P8A11


title: SomMuscle_P8B4


title: SomMuscle_P8B5


title: SomMuscle_P8A10


title: SomMuscle_P8A5


title: SomMuscle_P8B2


title: SomMuscle_P8A1


title: SomMuscle_P6H10


title: SomMuscle_P6H4


title: SomMuscle_P6G10


title: SomMuscle_P6H8


title: SomMuscle_P8C2


title: SomMuscle_P8A8


title: SomMuscle_P6G7


title: SomMuscle_P6G8


title: SomMuscle_P6G5


title: SomMuscle_P6G3


title: SomMuscle_P6G2


title: SomMuscle_P6F11


title: SomMuscle_P6F6


title: SomMuscle_P6F8


title: SomMuscle_P6F4


title: SomMuscle_P6F5


title: SomMuscle_P6E10


title: SomMuscle_P6F2


title: SomMuscle_P6E9


title: SomMuscle_P6E8


title: SomMuscle_P6E6


title: SomMuscle_P6E2


title: SomMuscle_P6E7


title: SomMuscle_P6E5


title: SomMuscle_P6E1


title: SomMuscle_P6H9


title: SomMuscle_P6D11


title: SomMuscle_P6D7


title: SomMuscle_P6D10


title: SomMuscle_P6D1


title: SomMuscle_P6B11


title: SomMuscle_P6C6


title: SomMuscle_P6D9


title: SomMuscle_P6B5


title: SomMuscle_P6D4


title: SomMuscle_P6C1


title: SomMuscle_P6B2


title: SomMuscle_P6D6


title: SomMuscle_P6A7


title: SomMuscle_P6E11


title: SomMuscle_P6C5


title: SomMuscle_P6C9


title: SomMuscle_P6B10


title: SomMuscle_P6C4


title: SomMuscle_P6B8


title: SomMuscle_P6B6


title: Control-vehicle-rep3

value: Sprague-Dawley

value: Vehicle


title: SomMuscle_P6C7


title: SomMuscle_P6A3


title: SomMuscle_P6B9


title: SomMuscle_P17H11


title: SomMuscle_P6A2


title: SomMuscle_P17G12


title: SomMuscle_P6A9


title: SomMuscle_P17H5


title: SomMuscle_P17G10


title: SomMuscle_P6C2


title: SomMuscle_P6A8


title: SomMuscle_P17G5


title: SomMuscle_P17G6


title: SomMuscle_P17G11


title: SomMuscle_P17G1


title: SomMuscle_P17G7


title: SomMuscle_P17G4


title: SomMuscle_P17G2


title: SomMuscle_P17F11


title: SomMuscle_P17F9


title: SomMuscle_P17F3


title: SomMuscle_P17F4


title: SomMuscle_P17F2


title: SomMuscle_P17F5


title: SomMuscle_P17E12


title: SomMuscle_P17F8


title: SomMuscle_P17F1


title: SomMuscle_P17E9


title: SomMuscle_P17E8


title: SomMuscle_P17E10


title: SomMuscle_P17E6


title: SomMuscle_P17E7


title: SomMuscle_P17F10


title: SomMuscle_P17E3


title: SomMuscle_P17D12


title: SomMuscle_P17E1


title: SomMuscle_P17D8


title: SomMuscle_P17D11


title: SomMuscle_P17D7


title: SomMuscle_P17D9


title: SomMuscle_P17E2


title: SomMuscle_P17C9


title: SomMuscle_P17C11


title: SomMuscle_P17C7


title: SomMuscle_P17C3


title: SomMuscle_P17C8


title: SomMuscle_P17C12


title: SomMuscle_P17C6


title: SomMuscle_P17E11


title: SomMuscle_P17C10


title: SomMuscle_P17C2


title: SomMuscle_P17B11


title: SomMuscle_P17D6


title: SomMuscle_P17C1


title: SomMuscle_P17E4


title: SomMuscle_P17D5


title: SomMuscle_P17B8


title: SomMuscle_P17B6


title: SomMuscle_P17D2


title: SomMuscle_P17B5


title: SomMuscle_P17D1


title: SomMuscle_P17B4


title: SomMuscle_P17A5


title: SomMuscle_P17A7


title: SomMuscle_P17B7


title: SomMuscle_P17A8


title: SomMuscle_P17A11


title: SomMuscle_P17A9


title: SomMuscle_P17A4


title: SomMuscle_P17A2


title: SomMuscle_P17A3


title: SomMuscle_P16H4


title: SomMuscle_P16G5


title: SomMuscle_P16H2


title: SomMuscle_P16G10


title: SomMuscle_P16G7


title: SomMuscle_P17A1


title: SomMuscle_P16G2


title: SomMuscle_P16F12


title: SomMuscle_P16F11


title: SomMuscle_P16G1


title: SomMuscle_P16F5


title: SomMuscle_P16F3


title: SomMuscle_P16F9


title: SomMuscle_P16F1


title: SomMuscle_P16F8


title: SomMuscle_P16F2


title: SomMuscle_P16E11


title: SomMuscle_P16E7


title: SomMuscle_P16E9


title: SomMuscle_P16E6


title: SomMuscle_P16E5


title: SomMuscle_P16G8


title: SomMuscle_P16E12


title: SomMuscle_P16E2


title: SomMuscle_P16G11


title: SomMuscle_P16D10


title: SomMuscle_P16D7


title: SomMuscle_P16D8


title: SomMuscle_P16D4


title: SomMuscle_P16D11


title: SomMuscle_P16C12


title: SomMuscle_P16D5


title: SomMuscle_P16C11


title: SomMuscle_P16C10


title: SomMuscle_P16C9


title: SomMuscle_P16E10


title: SomMuscle_P16C5


title: SomMuscle_P16C3


title: SomMuscle_P16B11


title: SomMuscle_P16C1


title: SomMuscle_P16D2


title: SomMuscle_P16B3


title: SomMuscle_P16B5


title: SomMuscle_P16A12


title: SomMuscle_P16A11


title: SomMuscle_P16C4


title: SomMuscle_P16A8


title: SomMuscle_P16A7


title: SomMuscle_P15H9


title: SomMuscle_P16A2


title: SomMuscle_P15H7


title: SomMuscle_P16B2


title: SomMuscle_P16B7


title: SomMuscle_P16B10


title: SomMuscle_P15H3


title: SomMuscle_P15H4


title: SomMuscle_P16A5


title: SomMuscle_P15G10


title: SomMuscle_P15G8


title: SomMuscle_P15G7


title: SomMuscle_P15G3


title: SomMuscle_P15F10


title: SomMuscle_P15F9


title: SomMuscle_P15F7


title: SomMuscle_P15F6


title: SomMuscle_P15F4


title: SomMuscle_P15F3


title: SomMuscle_P15F1


title: SomMuscle_P15H6


title: SomMuscle_P15F2


title: SomMuscle_P15E11


title: SomMuscle_P15E8


title: SomMuscle_P15E5


title: SomMuscle_P15E6


title: SomMuscle_P15E1


title: SomMuscle_P15D10


title: SomMuscle_P15E2


title: SomMuscle_P15D4


title: SomMuscle_P15D9


title: SomMuscle_P6A6


title: SomMuscle_P15D11


title: SomMuscle_P15C12


title: SomMuscle_P15D1


title: SomMuscle_P15G6


title: SomMuscle_P15E4


title: SomMuscle_P15G5


title: SomMuscle_P15C11


title: SomMuscle_P15C8


title: SomMuscle_P16C8


title: SomMuscle_P15D3


title: SomMuscle_P15C7


title: SomMuscle_P15B11


title: SomMuscle_P15B6


title: SomMuscle_P15B4


title: SomMuscle_P15B5


title: SomMuscle_P15A9


title: SomMuscle_P15A6


title: SomMuscle_P15B2


title: SomMuscle_P15B3


title: SomMuscle_P15D7


title: SomMuscle_P15A7


title: SomMuscle_P15A5


title: SomMuscle_P14H11


title: SomMuscle_P14H12


title: SomMuscle_P14H8


title: SomMuscle_P14H3


title: SomMuscle_P15A3


title: SomMuscle_P14H5


title: SomMuscle_P14G8


title: SomMuscle_P14G11


title: SomMuscle_P14H7


title: SomMuscle_P14G9


title: SomMuscle_P14H6


title: SomMuscle_P14F10


title: SomMuscle_P14G12


title: SomMuscle_P14F7


title: SomMuscle_P14F9


title: SomMuscle_P14F6


title: SomMuscle_P14F3


title: SomMuscle_P14G3


title: SomMuscle_P14F2


title: SomMuscle_P14E12


title: SomMuscle_P14E9


title: SomMuscle_P14E11


title: SomMuscle_P14E7


title: SomMuscle_P14E6


title: SomMuscle_P14E5


title: SomMuscle_P14E2


title: SomMuscle_P14D12


title: SomMuscle_P14D11


title: SomMuscle_P14E3


title: SomMuscle_P14D9


title: SomMuscle_P14G7


title: SomMuscle_P14D8


title: SomMuscle_P14C10


title: SomMuscle_P14C8


title: SomMuscle_P14C9


title: SomMuscle_P14D5


title: SomMuscle_P14D4


title: SomMuscle_P14B7


title: SomMuscle_P14B11


title: SomMuscle_P14B5


title: SomMuscle_P14B12


title: SomMuscle_P14B10


title: SomMuscle_P14C4


title: SomMuscle_P14A12


title: SomMuscle_P14D6


title: SomMuscle_P14A4


title: SomMuscle_P14A6


title: SomMuscle_P14A10


title: SomMuscle_P14A11


title: SomMuscle_P13H11


title: SomMuscle_P14D10


title: SomMuscle_P14A9


title: SomMuscle_P13H10


title: SomMuscle_P13H5


title: SomMuscle_P14C6


title: SomMuscle_P14D7


title: SomMuscle_P13G11


title: SomMuscle_P13G10


title: SomMuscle_P13H8


title: SomMuscle_P14C11


title: SomMuscle_P13H4


title: SomMuscle_P13G7


title: SomMuscle_P13G3


title: SomMuscle_P13G9


title: SomMuscle_P13G2


title: SomMuscle_P13F9


title: SomMuscle_P13F12


title: SomMuscle_P13G8


title: SomMuscle_P13F7


title: SomMuscle_P14A3


title: SomMuscle_P13F3


title: SomMuscle_P13F4


title: SomMuscle_P13F5


title: SomMuscle_P13E11


title: SomMuscle_P13E10


title: SomMuscle_P13E12


title: SomMuscle_P13H7


title: SomMuscle_P13E2


title: SomMuscle_P13E8


title: SomMuscle_P13E5


title: SomMuscle_P13D12


title: SomMuscle_P13D6


title: SomMuscle_P13D4


title: SomMuscle_P13D11


title: SomMuscle_P13C10


title: SomMuscle_P13D7


title: SomMuscle_P13F8


title: SomMuscle_P13D1


title: SomMuscle_P13C7


title: SomMuscle_P13D9


title: SomMuscle_P13C6


title: SomMuscle_P13C5


title: SomMuscle_P13B11


title: SomMuscle_P13C2


title: SomMuscle_P13C9


title: SomMuscle_P13B10


title: SomMuscle_P13B8


title: SomMuscle_P13E4


title: SomMuscle_P13B7


title: SomMuscle_P13B2


title: SomMuscle_P13B5


title: SomMuscle_P13D8


title: SomMuscle_P13A9


title: SomMuscle_P13A8


title: SomMuscle_P13A7


title: SomMuscle_P13A6


title: SomMuscle_P12H8


title: SomMuscle_P12H9


title: SomMuscle_P12H7


title: SomMuscle_P12H3


title: SomMuscle_P13A4


title: SomMuscle_P12H2


title: SomMuscle_P13C1


title: SomMuscle_P13C8


title: SomMuscle_P13B9


title: SomMuscle_P12G10


title: SomMuscle_P12G9


title: SomMuscle_P12G7


title: SomMuscle_P12G8


title: SomMuscle_P12G6


title: SomMuscle_P12G4


title: SomMuscle_P12G11


title: SomMuscle_P13E9


title: SomMuscle_P12G3


title: SomMuscle_P13B4


title: SomMuscle_P12F12


title: SomMuscle_P13B6


title: SomMuscle_P12G2


title: SomMuscle_P12F7


title: SomMuscle_P12F6


title: SomMuscle_P12F5


title: SomMuscle_P12G12


title: SomMuscle_P12E5


title: SomMuscle_P12E10


title: SomMuscle_P12E6


title: SomMuscle_P12E4


title: SomMuscle_P12E3


title: SomMuscle_P12E12


title: SomMuscle_P12D10


title: SomMuscle_P12F1


title: SomMuscle_P12D9


title: SomMuscle_P12D2


title: SomMuscle_P12D4


title: SomMuscle_P12D8


title: SomMuscle_P12D12


title: SomMuscle_P12C11


title: SomMuscle_P12C7


title: SomMuscle_P12D1


title: SomMuscle_P12F9


title: SomMuscle_P12F10


title: SomMuscle_P12C5


title: SomMuscle_P12D6


title: SomMuscle_P12C4


title: SomMuscle_P12C6


title: SomMuscle_P12C3


title: SomMuscle_P12B12


title: SomMuscle_P12F3


title: SomMuscle_P12E1


title: SomMuscle_P12B8


title: SomMuscle_P12B3


title: SomMuscle_P12B5


title: SomMuscle_P12C10


title: SomMuscle_P12B7


title: SomMuscle_P12B2


title: SomMuscle_P12B6


title: SomMuscle_P12F8


title: SomMuscle_P12A7


title: SomMuscle_P12A8


title: SomMuscle_P12A10


title: SomMuscle_P12A11


title: SomMuscle_P12A9


title: SomMuscle_P12A6


title: SomMuscle_P12A5


title: SomMuscle_P11H6


title: SomMuscle_P12A3


title: SomMuscle_P11H4


title: SomMuscle_P11G11


title: SomMuscle_P11H1


title: SomMuscle_P11H3


title: SomMuscle_P11G7


title: SomMuscle_P11G8


title: SomMuscle_P11G5


title: SomMuscle_P11H5


title: SomMuscle_P11G6


title: SomMuscle_P11G10


title: SomMuscle_P11H11


title: SomMuscle_P11G4


title: SomMuscle_P11G2


title: SomMuscle_P11F8


title: SomMuscle_P11F9


title: SomMuscle_P12A4


title: SomMuscle_P11G1


title: SomMuscle_P11F7


title: SomMuscle_P11F1


title: SomMuscle_P11E11


title: SomMuscle_P11F5


title: SomMuscle_P11E6


title: SomMuscle_P11F6


title: SomMuscle_P11E4


title: SomMuscle_P11E8


title: SomMuscle_P11E2


title: SomMuscle_P11E1


title: SomMuscle_P11D10


title: SomMuscle_P11D9


title: SomMuscle_P11D8


title: SomMuscle_P11D1


title: SomMuscle_P11D5


title: SomMuscle_P11D2


title: SomMuscle_P11C11


title: SomMuscle_P11D3


title: SomMuscle_P11D4


title: SomMuscle_P11C9


title: SomMuscle_P11C4


title: SomMuscle_P11E10


title: SomMuscle_P11C2


title: SomMuscle_P11B9


title: SomMuscle_P11B7


title: SomMuscle_P11B8


title: SomMuscle_P11B11


title: SomMuscle_P11E3


title: SomMuscle_P11A9


title: SomMuscle_P11A8


title: SomMuscle_P11B2


title: SomMuscle_P11D7


title: SomMuscle_P11A3


title: SomMuscle_P11B3


title: SomMuscle_P11A5


title: SomMuscle_P11A7


title: SomMuscle_P11C6


title: SomMuscle_P11A4


title: SomMuscle_P10H6


title: SomMuscle_P10H5


title: SomMuscle_P10H7


title: SomMuscle_P10G9


title: SomMuscle_P10G10


title: SomMuscle_P10H4


title: SomMuscle_P11C3


title: SomMuscle_P10G5


title: SomMuscle_P11C1


title: SomMuscle_P10H2


title: SomMuscle_P10H8


title: SomMuscle_P11B4


title: SomMuscle_P10G12


title: SomMuscle_P10G2


title: SomMuscle_P10G3


title: SomMuscle_P10G4


title: SomMuscle_P10F5


title: SomMuscle_P10F4


title: SomMuscle_P10F10


title: SomMuscle_P10E11


title: SomMuscle_P10F2


title: SomMuscle_P10E6


title: SomMuscle_P10E8


title: SomMuscle_P10E9


title: SomMuscle_P10E4


title: SomMuscle_P10E1


title: SomMuscle_P10E10


title: SomMuscle_P10D11


title: SomMuscle_P10D10


title: SomMuscle_P10E5


title: SomMuscle_P10D1


title: SomMuscle_P10D3


title: SomMuscle_P10C11


title: SomMuscle_P10D5


title: SomMuscle_P10D7


title: SomMuscle_P10C7


title: SomMuscle_P10F12


title: SomMuscle_P10C10


title: SomMuscle_P10C8


title: SomMuscle_P10C2


title: SomMuscle_P10D8


title: SomMuscle_P10B11


title: SomMuscle_P10B9


title: SomMuscle_P10C5


title: SomMuscle_P10B5


title: SomMuscle_P10B3


title: SomMuscle_P10A9


title: SomMuscle_P10A11


title: SomMuscle_P10B7


title: SomMuscle_P5H10


title: SomMuscle_P10A5


title: SomMuscle_P5H12


title: SomMuscle_P5H8


title: SomMuscle_P5H4


title: SomMuscle_P5H9


title: SomMuscle_P5H6


title: SomMuscle_P5H1


title: SomMuscle_P10E12


title: SomMuscle_P5H2


title: SomMuscle_P10B10


title: SomMuscle_P5G11


title: SomMuscle_P5H3


title: SomMuscle_P5G7


title: SomMuscle_P5G8


title: SomMuscle_P5H7


title: SomMuscle_P10A8


title: SomMuscle_P10B6


title: SomMuscle_P10C4


title: SomMuscle_P10B1


title: SomMuscle_P5G5


title: SomMuscle_P5G12


title: SomMuscle_P5G4


title: SomMuscle_P5G1


title: SomMuscle_P5F12


title: SomMuscle_P5G2


title: SomMuscle_P5H5


title: SomMuscle_P5F10


title: SomMuscle_P5F8


title: SomMuscle_P10A7


title: SomMuscle_P5G9


title: SomMuscle_P5F9


title: SomMuscle_P5F7


title: SomMuscle_P5F2


title: SomMuscle_P5F6


title: SomMuscle_P5F3


title: SomMuscle_P5F1


title: SomMuscle_P5E5


title: SomMuscle_P5E8


title: SomMuscle_P5E9


title: SomMuscle_P5D10


title: SomMuscle_P5E12


title: SomMuscle_P5D8


title: SomMuscle_P5E2


title: SomMuscle_P5D5


title: SomMuscle_P5E1


title: SomMuscle_P5D11


title: SomMuscle_P5D12


title: SomMuscle_P5D7


title: SomMuscle_P5D4


title: SomMuscle_P5D1


title: SomMuscle_P5C11


title: SomMuscle_P5D3


title: SomMuscle_P5C12


title: SomMuscle_P5C7


title: SomMuscle_P5C9


title: SomMuscle_P5C2


title: SomMuscle_P5B12


title: SomMuscle_P5C3


title: SomMuscle_P5C5


title: SomMuscle_P5C1


title: SomMuscle_P5E10


title: SomMuscle_P5B10


title: SomMuscle_P5B9


title: SomMuscle_P5B7


title: SomMuscle_P5B8


title: SomMuscle_P5B6


title: SomMuscle_P5B4


title: SomMuscle_P5A12


title: SomMuscle_P5A11


title: SomMuscle_P5A4


title: SomMuscle_P5A5


title: SomMuscle_P5A7


title: SomMuscle_P5B2


title: SomMuscle_P5A10


title: SomMuscle_P3H10


title: SomMuscle_P5C10


title: SomMuscle_P3H11


title: SomMuscle_P3H9


title: SomMuscle_P3H6


title: SomMuscle_P3H8


title: SomMuscle_P3G12


title: SomMuscle_P3G11


title: SomMuscle_P3G7


title: SomMuscle_P3G9


title: SomMuscle_P3G6


title: SomMuscle_P3G4


title: SomMuscle_P3G2


title: SomMuscle_P3F8


title: SomMuscle_P3F9


title: SomMuscle_P3F10


title: SomMuscle_P3F5


title: SomMuscle_P3F3


title: SomMuscle_P3F2


title: SomMuscle_P3E12


title: SomMuscle_P3H3


title: SomMuscle_P3E6


title: SomMuscle_P3H5


title: SomMuscle_P3E9


title: SomMuscle_P3E3


title: SomMuscle_P3D12


title: SomMuscle_P3E7


title: SomMuscle_P3D11


title: SomMuscle_P3E1


title: SomMuscle_P3G8


title: SomMuscle_P3D6


title: SomMuscle_P3D3


title: SomMuscle_P3D8


title: SomMuscle_P3F11


title: SomMuscle_P3C12


title: SomMuscle_P3E8


title: SomMuscle_P3E5


title: SomMuscle_P3C11


title: SomMuscle_P3C10


title: SomMuscle_P3F6


title: SomMuscle_P3D2


title: SomMuscle_P3C7


title: SomMuscle_P3C5


title: SomMuscle_P3C6


title: SomMuscle_P3G10


title: SomMuscle_P3C4


title: SomMuscle_P3C3


title: SomMuscle_P3D1


title: SomMuscle_P3C1


title: SomMuscle_P3C2


title: SomMuscle_P3B6


title: SomMuscle_P3B4


title: SomMuscle_P3A8


title: SomMuscle_P3B3


title: SomMuscle_P3B8


title: SomMuscle_P3A6


title: SomMuscle_P3A10


title: SomMuscle_P3B11


title: SomMuscle_P3B7


title: SomMuscle_P3A5


title: SomMuscle_P2H6


title: SomMuscle_P2G12


title: SomMuscle_P2G8


title: SomMuscle_P3A4


title: SomMuscle_P3C9


title: SomMuscle_P2G9


title: SomMuscle_P2G5


title: SomMuscle_P2G6


title: SomMuscle_P2G1


title: SomMuscle_P2G2


title: SomMuscle_P2G3


title: SomMuscle_P2F9


title: SomMuscle_P2F11


title: SomMuscle_P2F7


title: SomMuscle_P2F5


title: SomMuscle_P2F4


title: SomMuscle_P3B2


title: SomMuscle_P2F3


title: SomMuscle_P2F1


title: SomMuscle_P3A7


title: SomMuscle_P2F2


title: SomMuscle_P2E7


title: SomMuscle_P2E5


title: SomMuscle_P2E6


title: SomMuscle_P2E4


title: SomMuscle_P2E8


title: SomMuscle_P2D10


title: SomMuscle_P2E2


title: SomMuscle_P2D7


title: SomMuscle_P2E1


title: SomMuscle_P2D8


title: SomMuscle_P2D5


title: SomMuscle_P2D4


title: SomMuscle_P2C8


title: SomMuscle_P2C10


title: SomMuscle_P2C11


title: SomMuscle_P2C7


title: SomMuscle_P2C6


title: SomMuscle_P2B12


title: SomMuscle_P2C4


title: SomMuscle_P2C2


title: SomMuscle_P2C3


title: SomMuscle_P2G4


title: SomMuscle_P2B8


title: SomMuscle_P2B7


title: SomMuscle_P2B9


title: SomMuscle_P2B3


title: SomMuscle_P2B4


title: SomMuscle_P2A11


title: SomMuscle_P2D6


title: SomMuscle_P2A9


title: SomMuscle_P2A10


title: SomMuscle_P2A8


title: SomMuscle_P1H10


title: SomMuscle_P1H5


title: SomMuscle_P1H2


title: SomMuscle_P1H12


title: SomMuscle_P1G12


title: SomMuscle_P1G7


title: SomMuscle_P1G5


title: SomMuscle_P1G3


title: SomMuscle_P1G1


title: SomMuscle_P2C5


title: SomMuscle_P1F9


title: SomMuscle_P1F6


title: SomMuscle_P1F7


title: SomMuscle_P1E12


title: SomMuscle_P1E8


title: SomMuscle_P1F4


title: SomMuscle_P2A5


title: SomMuscle_P1E5


title: SomMuscle_P1H9


title: SomMuscle_P1E2


title: SomMuscle_P1E4


title: SomMuscle_P1E1


title: EB-Flag-Dox

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
ChIP-seq reads were trimmed and aligned to hg19 using bowtie2. Reads were normalized via RPKM and aggregate read signal for all coding genes was calculated in a 5k window centered at the TSS, using deepTools. Significance by first calculating average signal in 5k window for all TSS’, then comparing means across conditions via t-test.
Genome_build: Genome_build: UCSC hg19

source_name: WTC

extract_protocol:
Cells were dissociated using versene, washed once in cold PBS and counted. Approximately 6x10^6 cells were fixed and chromatin was PIXUL sonicated as described above. H3K27me3 (Active Motif Ab) Matrix-ChIP’ed DNA was  purified using phenol-chloroform extraction and ChIP-seq libraries were prepared (Next Gen DNA Library Kit, Active Motif, Cat# 53216, 53264).
Libraries were sequenced on NextSeq2000 in single end run and approximately 45 million raw reads were obtained for each sample.

value: iPSC WTC

tag: construct

value: EB-Flag


title: SomMuscle_P1D11


title: EBdCas9-Dox

tag: chip antibody


title: SomMuscle_P1E7


title: SomMuscle_P1D12


title: SomMuscle_P1D10


title: SomMuscle_P1D9


title: EBdCas9+dox_2

data_processing:
Reads were aligned using Hisat2(Kim et al., 2019) version 2.1.0, to version hg38 of the human genome with EBdCas9 sequence added.
Differentially expressed genes were identified with DESeq2
RNA-seq read counts were generated with featureCounts using Ensembl GRCH38 gene annotations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited file of gene-level transcript per million (TPM) for each sample.

growth_protocol: cells were grown in mTeSR1 stem cell media

extract_protocol:
RNA was extracted using Trizol (Life Technologies) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: hiPSCS

value: dox


title: EBdCas9+Dox

tag: cell type


title: EB-Flag+Dox


title: SomMuscle_P1G2

value: Mhc-GFP+ DAPI- DRAQ5+


title: SomMuscle_P1D4


title: SomMuscle_P1H6


title: SomMuscle_P1D2


title: EBdCas9+dox_1


title: EBdCas9-dox_2

value: no dox


title: SomMuscle_P1D1


title: SomMuscle_P1E6


title: EBdCas9-dox_1


title: SomMuscle_P1C12


title: SomMuscle_P1C11


title: SomMuscle_P1C10


title: SomMuscle_P1C9


title: SomMuscle_P1C8


title: SomMuscle_P1C7


title: SomMuscle_P1C5


title: SomMuscle_P1C3


title: SomMuscle_P1B9


title: SomMuscle_P1B12


title: SomMuscle_P1B8


title: SomMuscle_P1C1


title: SomMuscle_P1B7


title: MLL-AF9 Mbd2-/--3

city: Wuhan

first: Kuangguo

last: Zhou

state: Hubei

address: 1095 Jiefang Avenue

institute: Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: GFP+ BM leukemia cells of Mbd2 deletion

hyb_protocol: Following fragmentation, 12.5 μg of fragmented cRNA  were hybridized for 16 hr at 45℃ on Affymetrix GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: leukemia cells from Mbd2 Deletion MLL-AF9 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from more than 1 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Leukemic cells were obtained from mice transplanted with WT or Mbd2-/- AML cells for microarray analysis to compare their global gene expression profiles

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Fluorescence activated cell sorter (FACS, Aria Cell Sorter, BD Biosciences) was used to sort the specific cell population, and RNA was extracted with TRIzol reagent.

value: GFP+ BM leukemia cells

value: Mbd2 deletion


title: MLL-AF9 Mbd2-/--2

description: GFP+ BM leukemia cells of Mbd2 deletion


title: MLL-AF9 wild type-1

description: GFP+ BM leukemia cells of Mbd2 wild type

source_name: leukemia cells from Mbd2 wild-type MLL-AF9 mice

value: Mbd2 wild type


title: MLL-AF9 Mbd2-/--1

description: GFP+ BM leukemia cells of Mbd2 deletion


title: MLL-AF9 wild type-3


title: 3256_wk0_HYP_p1_F02_CC

city: Kensington

first: Jerome

last: Samir

state: NSW

address: Level 5, Wallace Wurth Building, High Street

department: IVPP

country: Australia

institute: Kirby Institute

data_processing:
Illumina NextSeq was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary_files_format_and_content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

source_name: CD8+ T cell

extract_protocol:
Single HCV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

tag: epitope

value: HYP

tag: dpi

value: CD8+ T cell


title: 3256_wk0_HYP_p1_C01_CC


title: 3256_wk0_HYP_p1_D02_CC


title: 3256_wk0_HYP_p1_D01_CC


title: 3256_wk0_HYP_p1_G02_CC


title: 3256_wk0_HYP_p1_E01_CC


title: 3256_wk0_HYP_p1_B02_CC


title: 3256_wk0_HYP_p1_G01_CC


title: SomMuscle_P1A7


title: 3256_wk0_HYP_p1_F01_CC


title: 3256_wk0_HYP_p1_B01_CC


title: SomMuscle_P1A5


title: MLL-AF9 wild type-2


title: 3256_wk0_HYP_p1_A02_CC


title: 3256_wk0_HYP_p1_E02_CC


title: SomMuscle_P1B4


title: SomMuscle_P1B6


title: 3256_wk0_HYP_p1_C02_CC


title: 3256_wk0_HYP_p1_A01_CC


title: SomMuscle_P1A11


title: Motoneuron_P17H11

source_name: Motoneuron

value: Ok371>RFP+ DAPI- DRAQ5+


title: SomMuscle_P1A10


title: MCRL_wk104_GPR_p1_G12_AE

value: CL-MCRL

value: GPR


title: MCRL_wk104_GPR_p1_D12_AE


title: Motoneuron_P17H8


title: Motoneuron_P17H6


title: MCRL_wk104_GPR_p1_C11_AE


title: Motoneuron_P17H4


title: MCRL_wk104_GPR_p1_C12_AE


title: Motoneuron_P17G12


title: MCRL_wk104_GPR_p1_A10_AE


title: MCRL_wk104_GPR_p1_E11_AE


title: MCRL_wk104_GPR_p1_F09_AE


title: MCRL_wk104_GPR_p1_H09_AE


title: Motoneuron_P17F10


title: Motoneuron_P17F9


title: Motoneuron_P17F7


title: Motoneuron_P17F8


title: MCRL_wk104_GPR_p1_B09_AE


title: Motoneuron_P17F6


title: Motoneuron_P17F4


title: MCRL_wk104_GPR_p1_B07_AE


title: MCRL_wk104_GPR_p1_H08_AE


title: MCRL_wk104_GPR_p1_A09_AE


title: Motoneuron_P17F2


title: Motoneuron_P17F12


title: MCRL_wk104_GPR_p1_F06_AE


title: MCRL_wk104_GPR_p1_H06_AE


title: Motoneuron_P17E12


title: Motoneuron_P17F1


title: MCRL_wk104_GPR_p1_E06_AE


title: Motoneuron_P17E11


title: Motoneuron_P17E10


title: MCRL_wk104_GPR_p1_C06_AE


title: MCRL_wk104_GPR_p1_B06_AE


title: Motoneuron_P17E9


title: MCRL_wk104_GPR_p1_A06_AE


title: Motoneuron_P17E8


title: MCRL_wk104_GPR_p1_D06_AE


title: MCRL_wk4_GPR_p2_G05_AE


title: Motoneuron_P17E5


title: Motoneuron_P17E6


title: Motoneuron_P17E4


title: MCRL_wk4_GPR_p2_D09_AE


title: Motoneuron_P17E7


title: MCRL_wk4_GPR_p2_B09_AE


title: MCRL_wk104_GPR_p1_B12_AE


title: MCRL_wk4_GPR_p2_A09_AE


title: Motoneuron_P17D12


title: Motoneuron_P17D11


title: Motoneuron_P17E2


title: MCRL_wk4_GPR_p2_F08_AE


title: Motoneuron_P17D9


title: MCRL_wk4_GPR_p2_E08_AE


title: MCRL_wk4_GPR_p2_D08_AE


title: MCRL_wk4_GPR_p2_C08_AE


title: Motoneuron_P17D6


title: MCRL_wk4_GPR_p2_A08_AE


title: Motoneuron_P17D5


title: MCRL_wk4_GPR_p2_B08_AE


title: MCRL_wk4_GPR_p2_D07_AE


title: MCRL_wk4_GPR_p2_F09_AE


title: Motoneuron_P17D4


title: MCRL_wk4_GPR_p2_C07_AE


title: Motoneuron_P17D7


title: MCRL_wk4_GPR_p2_B07_AE


title: Motoneuron_P17D2


title: Motoneuron_P17D1


title: MCRL_wk4_GPR_p2_B06_AE


title: Motoneuron_P17C11


title: MCRL_wk4_GPR_p2_D05_AE


title: Motoneuron_P17C10


title: Motoneuron_P17C8


title: MCRL_wk104_GPR_p2_G04_AE


title: MCRL_wk104_GPR_p2_B12_AE


title: Motoneuron_P17H5


title: Motoneuron_P17D8


title: MCRL_wk104_GPR_p2_G11_AE


title: Motoneuron_P17C7


title: Motoneuron_P17C6


title: MCRL_wk104_GPR_p2_B09_AE


title: MCRL_wk104_GPR_p2_C08_AE


title: Motoneuron_P17C2


title: MCRL_wk104_GPR_p2_B08_AE


title: MCRL_wk104_GPR_p2_C07_AE


title: Motoneuron_P17C1


title: Motoneuron_P17C5


title: Motoneuron_P17B8


title: MCRL_wk104_GPR_p2_A07_AE


title: MCRL_wk104_GPR_p2_B07_AE


title: MCRL_wk104_GPR_p2_E06_AE


title: Motoneuron_P17B6


title: MCRL_wk104_GPR_p2_F04_AE


title: Motoneuron_P17B4


title: MCRL_wk104_GPR_p2_A05_AE


title: MCRL_wk104_GPR_p2_B05_AE


title: MCRL_wk104_GPR_p2_E04_AE


title: Motoneuron_P17A12


title: Motoneuron_P17B5


title: MCRL_wk104_GPR_p2_D04_AE


title: Motoneuron_P17A11


title: MCRL_wk104_GPR_p2_B04_AE


title: Motoneuron_P17A9


title: MCRL_wk104_GPR_p2_C04_AE


title: Motoneuron_P17A7


title: MCRL_wk104_GPR_p2_G03_AE


title: MCRL_wk104_GPR_p2_A04_AE


title: Motoneuron_P17B11


title: Motoneuron_P17A4


title: MCRL_wk104_GPR_p2_G02_AE


title: Motoneuron_P17A6


title: Motoneuron_P17B7


title: MCRL_wk4_ATD_p1_E08_AE

value: ATD


title: Motoneuron_P17A2


title: Motoneuron_P17A3


title: MCRL_wk4_ATD_p1_F08_AE


title: Motoneuron_P16H10


title: MCRL_wk4_ATD_p1_G08_AE


title: Motoneuron_P16H11


title: Motoneuron_P17B3


title: Motoneuron_P16H8


title: MCRL_wk4_GPR_p2_C05_AE


title: MCRL_wk4_GPR_p2_A05_AE


title: Motoneuron_P16H2


title: Motoneuron_P16G12


title: Motoneuron_P16G11


title: MCRL_wk4_ATD_p1_G07_AE


title: MCRL_wk4_GPR_p2_E02_AE


title: MCRL_wk4_GPR_p1_F11_AE


title: Motoneuron_P16G10


title: Motoneuron_P16G9


title: MCRL_wk4_GPR_p1_E11_AE


title: MCRL_wk4_GPR_p1_D11_AE


title: Motoneuron_P16G7


title: MCRL_wk4_GPR_p1_A11_AE


title: Motoneuron_P16G8


title: MCRL_wk4_GPR_p1_F10_AE


title: Motoneuron_P16G3


title: MCRL_wk4_GPR_p2_B05_AE


title: Motoneuron_P16H9


title: MCRL_wk4_GPR_p1_E10_AE


title: MCRL_wk4_GPR_p1_D10_AE


title: Motoneuron_P16F11


title: Motoneuron_P16F10


title: MCRL_wk4_GPR_p1_C10_AE


title: MCRL_wk4_GPR_p1_A08_AE


title: MCRL_wk4_ATD_p1_G05_AE


title: Motoneuron_P16F8


title: Motoneuron_P16F7


title: MCRL_wk4_GPR_p1_F07_AE


title: MCRL_wk4_GPR_p1_G08_AE


title: Motoneuron_P16F5


title: MCRL_wk4_GPR_p1_F05_AE


title: MCRL_wk4_GPR_p1_A05_AE


title: Motoneuron_P16F4


title: MCRL_wk4_GPR_p1_E04_AE


title: MCRL_wk4_GPR_p1_F04_AE


title: Motoneuron_P16F2


title: Motoneuron_P16E12


title: MCRL_wk4_GPR_p1_F02_AE


title: Motoneuron_P16G2


title: MCRL_wk4_GPR_p1_F01_AE


title: Motoneuron_P16E10


title: MCRL_wk4_GPR_p1_D04_AE


title: Motoneuron_P16E9


title: MCRL_wk4_GPR_p1_C01_AE


title: MCRL_wk4_ATD_p1_G04_AE


title: Motoneuron_P16E8


title: MCRL_wk4_ATD_p2_G06_AE


title: Motoneuron_P16E3


title: MCRL_wk4_ATD_p2_D10_AE


title: MCRL_wk4_GPR_p1_D01_AE


title: MCRL_wk4_ATD_p2_B10_AE


title: Motoneuron_P16D10


title: Motoneuron_P16E7


title: MCRL_wk4_ATD_p2_F09_AE


title: MCRL_wk4_ATD_p2_E09_AE


title: Motoneuron_P16D11


title: Motoneuron_P16D9


title: Motoneuron_P16D8


title: Motoneuron_P16E11


title: Motoneuron_P16F3


title: Motoneuron_P16D5


title: MCRL_wk4_ATD_p2_A09_AE


title: Motoneuron_P16D4


title: Motoneuron_P16D7


title: MCRL_wk4_ATD_p2_D09_AE


title: MCRL_wk4_ATD_p2_F08_AE


title: Motoneuron_P16D3


title: Motoneuron_P16D12


title: MCRL_wk4_ATD_p1_F04_AE


title: Motoneuron_P16C12


title: MCRL_wk4_ATD_p2_D08_AE


title: MCRL_wk4_ATD_p2_C08_AE


title: MCRL_wk4_ATD_p2_B07_AE


title: Motoneuron_P16C8


title: Motoneuron_P16C10


title: MCRL_wk4_ATD_p2_B06_AE


title: MCRL_wk4_ATD_p2_A07_AE


title: MCRL_wk4_ATD_p2_B05_AE


title: Motoneuron_P16B12


title: MCRL_wk4_ATD_p2_G04_AE


title: Motoneuron_P16B10


title: MCRL_wk4_ATD_p2_A05_AE


title: Motoneuron_P16C3


title: Motoneuron_P16B9


title: Motoneuron_P16B11


title: MCRL_wk4_ATD_p2_E08_AE


title: MCRL_wk4_ATD_p2_B04_AE


title: Motoneuron_P16B8


title: MCRL_wk4_ATD_p2_A02_AE


title: MCRL_wk4_ATD_p1_E04_AE


title: MCRL_wk4_ATD_p2_G03_AE


title: Motoneuron_P16F12


title: Motoneuron_P16B6


title: Motoneuron_P16B5


title: Motoneuron_P16B7


title: MCRL_wk4_ATD_p1_G12_AE


title: Motoneuron_P16C6


title: MCRL_wk4_ATD_p1_G11_AE


title: MCRL_wk4_ATD_p1_F12_AE


title: Motoneuron_P16B3


title: MCRL_wk4_ATD_p1_F11_AE


title: Motoneuron_P16A11


title: MCRL_wk4_ATD_p1_E11_AE


title: Motoneuron_P16A10


title: Motoneuron_P16A9


title: Motoneuron_P16A4


title: MCRL_wk4_ATD_p1_C11_AE


title: MCRL_wk4_ATD_p1_B11_AE


title: Motoneuron_P16A3


title: MCRL_wk4_ATD_p1_A11_AE


title: Motoneuron_P15H2


title: MCRL_wk4_ATD_p1_F09_AE


title: Motoneuron_P15H11


title: Motoneuron_P15G12


title: MCRL_wk4_GPR_P1_C11_AE


title: MCRL_wk4_GPR_P1_C08_AE


title: MCRL_wk4_ATD_p1_A04_AE


title: Motoneuron_P15G10


title: MCRL_wk4_GPR_P1_C07_AE


title: Motoneuron_P16B4


title: Motoneuron_P16B2


title: Motoneuron_P15G7


title: Motoneuron_P15G9


title: MCRL_wk4_GPR_P1_B11_AE


title: Motoneuron_P15F12


title: Motoneuron_P15F11


title: MCRL_wk4_GPR_P1_B07_AE


title: MCRL_wk4_ATD_p1_D11_AE


title: Motoneuron_P15G3


title: MCRL_wk4_GPR_P1_A07_AE


title: MCRL_wk4_GPR_P1_B10_AE


title: MCRL_wk4_GPR_p1_A02_AE


title: Motoneuron_P15F10


title: MCRL_wk4_GPR_p1_C02_AE


title: MCRL_wk4_GPR_p1_F08_AE


title: MCRL_wk4_GPR_p1_E08_AE


title: Motoneuron_P15F7


title: MCRL_wk4_GPR_p1_E07_AE


title: Motoneuron_P15F5


title: Motoneuron_P15F4


title: Motoneuron_P15F3


title: Motoneuron_P15E12


title: MCRL_wk4_GPR_p1_E06_AE


title: MCRL_wk4_GPR_p1_E05_AE


title: Motoneuron_P15E11


title: MCRL_wk4_GPR_p1_E01_AE


title: MCRL_wk4_GPR_p1_D07_AE


title: MCRL_wk4_GPR_p1_D08_AE


title: Motoneuron_P15E8


title: Motoneuron_P15E7


title: MCRL_wk4_GPR_p1_D06_AE


title: MCRL_wk4_ATD_p1_G10_AE


title: MCRL_wk4_GPR_p1_D05_AE


title: Motoneuron_P15F9


title: Motoneuron_P15E3


title: Motoneuron_P15F8


title: Motoneuron_P15E2


title: Motoneuron_P15E6


title: MCRL_wk4_ATD_p1_F06_AE


title: Motoneuron_P17H12


title: Motoneuron_P15D11


title: Motoneuron_P15D9


title: MCRL_wk4_ATD_p1_E10_AE


title: MCRL_wk4_GPR_p1_E02_AE


title: MCRL_wk4_ATD_p1_E09_AE


title: Motoneuron_P15D5


title: MCRL_wk4_ATD_p1_D12_AE


title: MCRL_wk4_ATD_p1_D08_AE


title: Motoneuron_P15C10


title: Motoneuron_P15C9


title: Motoneuron_P15C8


title: MCRL_wk4_ATD_p1_E05_AE


title: Motoneuron_P15C12


title: MCRL_wk4_ATD_p1_D06_AE


title: Motoneuron_P15C5


title: MCRL_wk4_ATD_p1_C06_AE


title: MCRL_wk4_ATD_p1_F02_AE


title: MCRL_wk4_ATD_p1_B08_AE


title: Motoneuron_P15C4


title: Motoneuron_P15B10


title: MCRL_wk4_ATD_p1_B10_AE


title: MCRL_wk4_ATD_p1_D07_AE


title: Motoneuron_P15D6


title: Motoneuron_P15D3


title: MCRL_wk4_ATD_p1_B04_AE


title: MCRL_wk4_ATD_p1_A10_AE


title: Motoneuron_P15B2


title: Motoneuron_P15D8


title: MCRL_wk4_ATD_p1_E06_AE


title: MCRL_wk4_ATD_p1_C08_AE


title: Motoneuron_P15B8


title: Motoneuron_P15A11


title: MCRL_wk4_ATD_p1_A08_AE


title: MCRL_wk4_ATD_p1_A06_AE


title: MCRL_wk104_GPR_p2_H06_AE


title: Motoneuron_P15A6


title: Motoneuron_P15A7


title: Motoneuron_P15C3


title: Motoneuron_P15A4


title: MCRL_wk104_GPR_p2_G07_AE


title: Motoneuron_P15A10


title: Motoneuron_P15B7


title: Motoneuron_P15A3


title: Motoneuron_P14H8


title: Motoneuron_P14H9


title: MCRL_wk4_ATD_p1_B07_AE


title: Motoneuron_P14H12


title: MCRL_wk104_GPR_p2_D12_AE


title: MCRL_wk104_GPR_p2_F08_AE


title: MCRL_wk104_GPR_p2_E03_AE


title: MCRL_wk104_GPR_p2_C03_AE


title: Motoneuron_P14G12


title: MCRL_wk104_GPR_p2_A06_AE


title: Motoneuron_P14G11


title: Motoneuron_P14H2


title: Motoneuron_P14G10


title: MCRL_wk104_GPR_p2_F06_AE


title: MCRL_wk104_GPR_p1_G10_AE


title: MCRL_wk104_GPR_p2_C02_AE


title: MCRL_wk104_GPR_p1_G09_AE


title: Motoneuron_P14G9


title: MCRL_wk104_GPR_p1_F11_AE


title: Motoneuron_P14G7


title: MCRL_wk104_GPR_p2_G05_AE


title: MCRL_wk104_GPR_p1_F07_AE


title: Motoneuron_P14G6


title: Motoneuron_P14G5


title: MCRL_wk104_GPR_p1_C10_AE


title: MCRL_wk104_GPR_p1_C09_AE


title: Motoneuron_P14G4


title: MCRL_wk104_GPR_p1_A03_AE


title: MCRL_wk104_ATD_p2_H10_AE


title: MCRL_wk104_ATD_p2_H11_AE


title: Motoneuron_P14G2


title: Motoneuron_P14F12


title: MCRL_wk104_GPR_p1_A11_AE


title: Motoneuron_P14F11


title: Motoneuron_P14G3


title: Motoneuron_P14F10


title: Motoneuron_P14F9


title: MCRL_wk104_ATD_p2_H09_AE


title: Motoneuron_P14G8


title: MCRL_wk104_ATD_p2_H01_AE


title: Motoneuron_P14F6


title: Motoneuron_P14F5


title: Motoneuron_P14F8


title: MCRL_wk104_ATD_p2_H05_AE


title: MCRL_wk104_ATD_p2_H06_AE


title: Motoneuron_P14F4


title: MCRL_wk104_ATD_p2_G10_AE


title: MCRL_wk104_ATD_p2_G09_AE


title: MCRL_wk104_ATD_p2_G06_AE


title: MCRL_wk104_ATD_p2_G05_AE


title: Motoneuron_P14F3


title: Motoneuron_P14F2


title: MCRL_wk104_ATD_p2_G04_AE


title: Motoneuron_P14E10


title: MCRL_wk104_ATD_p2_G03_AE


title: Motoneuron_P14E9


title: MCRL_wk104_ATD_p2_G11_AE


title: Motoneuron_P14E8


title: MCRL_wk104_ATD_p2_G01_AE


title: MCRL_wk104_ATD_p2_F11_AE


title: Motoneuron_P14E7


title: MCRL_wk104_ATD_p2_F12_AE


title: Motoneuron_P14E5


title: MCRL_wk104_ATD_p2_F10_AE


title: Motoneuron_P14E6


title: Motoneuron_P14E3


title: MCRL_wk104_ATD_p2_F06_AE


title: MCRL_wk104_ATD_p2_F08_AE


title: Motoneuron_P14E4


title: MCRL_wk104_ATD_p2_F05_AE


title: Motoneuron_P14E1


title: MCRL_wk104_ATD_p2_F09_AE


title: MCRL_wk104_ATD_p2_F04_AE


title: Motoneuron_P14E2


title: MCRL_wk104_ATD_p2_F02_AE


title: Motoneuron_P14D12


title: Motoneuron_P14E11


title: Motoneuron_P14D11


title: MCRL_wk104_ATD_p2_F01_AE


title: Motoneuron_P14D9


title: MCRL_wk104_ATD_p2_E12_AE


title: MCRL_wk104_ATD_p2_E10_AE


title: MCRL_wk104_ATD_p2_E11_AE


title: Motoneuron_P14D7


title: MCRL_wk104_ATD_p2_E09_AE


title: MCRL_wk104_ATD_p2_E05_AE


title: Motoneuron_P14D6


title: Motoneuron_P14D5


title: MCRL_wk104_ATD_p2_E06_AE


title: MCRL_wk104_ATD_p2_E04_AE


title: Motoneuron_P14D4


title: Motoneuron_P14C12


title: MCRL_wk104_ATD_p2_E02_AE


title: Motoneuron_P14C10


title: Motoneuron_P14D2


title: MCRL_wk104_ATD_p2_E03_AE


title: Motoneuron_P14C11


title: Motoneuron_P14D10


title: Motoneuron_P14C9


title: MCRL_wk104_ATD_p2_D10_AE


title: Motoneuron_P14C8


title: MCRL_wk104_ATD_p2_E01_AE


title: MCRL_wk104_ATD_p2_D12_AE


title: MCRL_wk104_ATD_p2_D11_AE


title: MCRL_wk104_ATD_p2_D08_AE


title: Motoneuron_P14D8


title: MCRL_wk104_ATD_p2_D09_AE


title: Motoneuron_P14C7


title: MCRL_wk104_ATD_p2_D05_AE


title: MCRL_wk104_ATD_p2_D06_AE


title: Motoneuron_P14C5


title: MCRL_wk104_ATD_p2_D04_AE


title: Motoneuron_P14C6


title: Motoneuron_P14C3


title: Motoneuron_P14D3


title: Motoneuron_P14C4


title: MCRL_wk104_ATD_p2_D03_AE


title: Motoneuron_P14C1


title: MCRL_wk104_ATD_p2_D02_AE


title: Motoneuron_P14C2


title: MCRL_wk104_ATD_p2_D01_AE


title: Motoneuron_P14B12


title: MCRL_wk104_ATD_p2_C11_AE


title: MCRL_wk104_ATD_p2_C10_AE


title: MCRL_wk104_ATD_p2_C09_AE


title: Motoneuron_P14B10


title: Motoneuron_P14B8


title: Motoneuron_P14B11


title: Motoneuron_P14B5


title: MCRL_wk104_ATD_p2_C03_AE


title: MCRL_wk104_ATD_p2_C02_AE


title: Motoneuron_P14B7


title: MCRL_wk104_ATD_p2_B12_AE


title: MCRL_wk104_ATD_p2_B10_AE


title: Motoneuron_P14A6


title: Motoneuron_P14A10


title: Motoneuron_P14A11


title: MCRL_wk104_ATD_p2_B11_AE


title: MCRL_wk104_ATD_p2_B09_AE


title: Motoneuron_P14A5


title: Motoneuron_P14A4


title: MCRL_wk104_ATD_p2_B08_AE


title: MCRL_wk104_ATD_p2_B04_AE


title: MCRL_wk104_ATD_p2_C12_AE


title: Motoneuron_P14A2


title: Motoneuron_P14A3


title: Motoneuron_P14B4


title: MCRL_wk104_ATD_p2_C06_AE


title: Motoneuron_P13H11


title: MCRL_wk104_ATD_p2_B02_AE


title: MCRL_wk0_GPR_p2_E06_AE


title: Motoneuron_P13H9


title: MCRL_wk0_GPR_p2_E05_AE


title: Motoneuron_P13H10


title: Motoneuron_P13H8


title: MCRL_wk0_GPR_p2_C06_AE


title: MCRL_wk0_GPR_p2_D07_AE


title: MCRL_wk0_GPR_p2_C03_AE


title: Motoneuron_P13H7


title: Motoneuron_P13H5


title: MCRL_wk0_GPR_p2_D09_AE


title: Motoneuron_P13H4


title: Motoneuron_P13H3


title: MCRL_wk0_GPR_p2_B06_AE


title: MCRL_wk0_GPR_p2_B05_AE


title: Motoneuron_P13G12


title: MCRL_wk0_GPR_p2_A09_AE


title: MCRL_wk104_ATD_p2_B03_AE


title: Motoneuron_P13H2


title: MCRL_wk0_GPR_p1_H09_AE


title: Motoneuron_P13G11


title: Motoneuron_P13G9


title: MCRL_wk0_GPR_p1_H03_AE


title: Motoneuron_P13G10


title: MCRL_wk0_GPR_p1_H01_AE


title: Motoneuron_P13H6


title: Motoneuron_P13G6


title: Motoneuron_P13G7


title: MCRL_wk0_GPR_p1_G07_AE


title: MCRL_wk0_GPR_p1_G12_AE


title: MCRL_wk0_GPR_p1_H02_AE


title: MCRL_wk0_GPR_p1_G03_AE


title: Motoneuron_P13G8


title: Motoneuron_P13G2


title: Motoneuron_P13G4


title: MCRL_wk0_GPR_p2_C02_AE


title: MCRL_wk0_GPR_p1_F12_AE


title: Motoneuron_P13G1


title: MCRL_wk0_GPR_p1_F10_AE


title: MCRL_wk0_GPR_p1_F09_AE


title: MCRL_wk0_GPR_p1_G02_AE


title: Motoneuron_P13F10


title: MCRL_wk0_GPR_p1_F04_AE


title: Motoneuron_P13F9


title: MCRL_wk0_GPR_p1_F06_AE


title: Motoneuron_P13F8


title: MCRL_wk0_GPR_p1_F07_AE


title: MCRL_wk0_GPR_p1_F03_AE


title: Motoneuron_P13F7


title: Motoneuron_P13F6


title: Motoneuron_P13F5


title: MCRL_wk0_GPR_p1_F01_AE


title: MCRL_wk0_GPR_p1_E03_AE


title: MCRL_wk0_GPR_p1_F02_AE


title: Motoneuron_P13F3


title: Motoneuron_P13F12


title: Motoneuron_P13E11


title: Motoneuron_P13F4


title: Motoneuron_P13F1


title: MCRL_wk0_GPR_p1_E12_AE


title: Motoneuron_P13F11


title: MCRL_wk0_GPR_p1_E07_AE


title: MCRL_wk0_GPR_p1_D12_AE


title: Motoneuron_P13E10


title: Motoneuron_P13E8


title: MCRL_wk0_GPR_p1_D10_AE


title: MCRL_wk0_GPR_p1_E01_AE


title: Motoneuron_P13E7


title: MCRL_wk0_GPR_p1_E02_AE


title: Motoneuron_P13E4


title: MCRL_wk0_GPR_p1_D06_AE


title: MCRL_wk0_GPR_p1_D02_AE


title: Motoneuron_P13E3


title: Motoneuron_P13E2


title: MCRL_wk0_GPR_p1_D01_AE


title: Motoneuron_P13D12


title: MCRL_wk0_GPR_p1_D04_AE


title: MCRL_wk0_GPR_p1_C11_AE


title: Motoneuron_P13E6


title: Motoneuron_P13D7


title: Motoneuron_P13D9


title: Motoneuron_P13D11


title: MCRL_wk0_GPR_p1_C08_AE


title: Motoneuron_P13D10


title: MCRL_wk0_GPR_p1_C05_AE


title: MCRL_wk0_GPR_p1_C04_AE


title: Motoneuron_P13D4


title: Motoneuron_P13C12


title: Motoneuron_P13D3


title: MCRL_wk0_GPR_p1_B04_AE


title: MCRL_wk0_GPR_p1_D09_AE


title: MCRL_wk0_GPR_p1_C02_AE


title: Motoneuron_P13D5


title: MCRL_wk0_GPR_p1_D03_AE


title: MCRL_wk0_GPR_p1_B06_AE


title: MCRL_wk0_GPR_p1_C07_AE


title: Motoneuron_P13D2


title: MCRL_wk0_GPR_p1_B01_AE


title: Motoneuron_P13C11


title: Motoneuron_P13C10


title: MCRL_wk0_GPR_p1_B02_AE


title: Motoneuron_P13C9


title: Motoneuron_P13D1


title: MCRL_wk0_GPR_p1_C09_AE


title: Motoneuron_P13C8


title: MCRL_wk0_GPR_p1_A07_AE


title: MCRL_wk0_GPR_p1_A02_AE


title: Motoneuron_P13C5


title: MCRL_wk0_GPR_p1_A01_AE


title: Motoneuron_P13C1


title: MCRL_wk0_ATD_p2_H06_AE


title: MCRL_wk0_ATD_p2_H05_AE


title: Motoneuron_P13B10


title: MCRL_wk0_ATD_p2_H11_AE


title: Motoneuron_P13B11


title: Motoneuron_P13C4


title: MCRL_wk0_ATD_p2_G06_AE


title: Motoneuron_P13B12


title: Motoneuron_P13B8


title: MCRL_wk0_ATD_p2_G09_AE


title: Motoneuron_P13B9


title: MCRL_wk0_ATD_p2_G05_AE


title: MCRL_wk0_ATD_p2_G01_AE


title: MCRL_wk0_ATD_p2_F11_AE


title: Motoneuron_P13B6


title: MCRL_wk0_ATD_p2_F10_AE


title: Motoneuron_P13B7


title: Motoneuron_P13B5


title: MCRL_wk0_ATD_p2_F08_AE


title: Motoneuron_P13B4


title: Motoneuron_P13C2


title: MCRL_wk0_ATD_p2_F09_AE


title: MCRL_wk0_ATD_p2_H09_AE


title: Motoneuron_P13B3


title: MCRL_wk0_ATD_p2_G10_AE


title: MCRL_wk0_ATD_p2_F05_AE


title: Motoneuron_P13A12


title: MCRL_wk0_ATD_p2_F04_AE


title: Motoneuron_P13A11


title: MCRL_wk0_ATD_p2_F03_AE


title: MCRL_wk0_ATD_p2_E12_AE


title: MCRL_wk0_ATD_p2_F01_AE


title: Motoneuron_P13A8


title: Motoneuron_P13A6


title: MCRL_wk0_ATD_p2_E10_AE


title: MCRL_wk0_ATD_p2_E11_AE


title: Motoneuron_P13A5


title: Motoneuron_P13A4


title: MCRL_wk0_ATD_p2_E08_AE


title: MCRL_wk0_ATD_p2_E09_AE


title: MCRL_wk0_ATD_p2_F06_AE


title: MCRL_wk0_ATD_p2_E05_AE


title: Motoneuron_P9H10


title: MCRL_wk0_ATD_p2_E04_AE


title: Motoneuron_P9H9


title: Motoneuron_P13A10


title: Motoneuron_P13B2


title: MCRL_wk0_ATD_p2_E03_AE


title: Motoneuron_P9H8


title: MCRL_wk0_ATD_p2_E01_AE


title: Motoneuron_P9H7


title: Motoneuron_P13A9


title: MCRL_wk0_ATD_p2_D12_AE


title: Motoneuron_P9H3


title: MCRL_wk0_ATD_p2_D10_AE


title: Motoneuron_P13A7


title: MCRL_wk0_ATD_p2_D09_AE


title: Motoneuron_P9H6


title: Motoneuron_P9H2


title: Motoneuron_P9H5


title: Motoneuron_P13A3


title: MCRL_wk0_ATD_p2_D06_AE


title: Motoneuron_P13A2


title: MCRL_wk0_ATD_p2_E06_AE


title: MCRL_wk0_ATD_p2_D08_AE


title: MCRL_wk0_ATD_p2_D05_AE


title: Motoneuron_P9H1


title: Motoneuron_P9G12


title: MCRL_wk0_ATD_p2_D04_AE


title: Motoneuron_P9F12


title: Motoneuron_P9G6


title: MCRL_wk0_ATD_p2_D01_AE


title: MCRL_wk0_ATD_p2_D02_AE


title: Motoneuron_P9F11


title: MCRL_wk0_ATD_p2_D11_AE


title: Motoneuron_P9G4


title: MCRL_wk0_ATD_p2_C10_AE


title: MCRL_wk0_ATD_p2_C12_AE


title: MCRL_wk0_ATD_p2_C11_AE


title: Motoneuron_P9F10


title: Motoneuron_P9F8


title: MCRL_wk0_ATD_p2_C05_AE


title: Motoneuron_P9F4


title: MCRL_wk0_ATD_p2_C03_AE


title: Motoneuron_P9G8


title: Motoneuron_P9E12


title: MCRL_wk0_ATD_p2_B12_AE


title: Motoneuron_P9F3


title: MCRL_wk0_ATD_p2_B11_AE


title: MCRL_wk0_ATD_p2_B10_AE


title: MCRL_wk0_ATD_p2_B08_AE


title: Motoneuron_P9F5


title: MCRL_wk0_ATD_p2_C08_AE


title: Motoneuron_P9E9


title: MCRL_wk0_ATD_p2_B06_AE


title: Motoneuron_P9E7


title: Motoneuron_P9E4


title: Motoneuron_P9E5


title: MCRL_wk0_ATD_p2_B05_AE


title: MCRL_wk0_ATD_p2_B04_AE


title: Motoneuron_P9D12


title: MCRL_wk0_ATD_p2_B02_AE


title: MCRL_wk0_ATD_p2_A11_AE


title: Motoneuron_P9D8


title: Motoneuron_P9D4


title: MCRL_wk0_ATD_p2_A10_AE


title: Motoneuron_P9D11


title: MCRL_wk0_ATD_p2_A12_AE


title: Motoneuron_P9E10


title: Motoneuron_P9C10


title: MCRL_wk0_ATD_p2_A04_AE


title: Motoneuron_P9C2


title: Motoneuron_P9B11


title: Motoneuron_P9D2


title: MCRL_wk0_ATD_p2_A01_AE


title: MCRL_wk0_ATD_p2_A09_AE


title: MCRL_wk0_ATD_p1_H03_AE


title: Motoneuron_P9C3


title: MCRL_wk0_ATD_p2_A05_AE


title: Motoneuron_P9B5


title: MCRL_wk0_ATD_p1_H09_AE


title: Motoneuron_P9B8


title: Motoneuron_P9B9


title: Motoneuron_P9E8


title: MCRL_wk0_ATD_p1_G06_AE


title: Motoneuron_P9B4


title: Motoneuron_P9A9


title: MCRL_wk0_ATD_p1_H02_AE


title: MCRL_wk0_ATD_p1_G05_AE


title: MCRL_wk0_ATD_p1_G02_AE


title: Motoneuron_P9A6


title: Motoneuron_P9A10


title: MCRL_wk0_ATD_p2_B03_AE


title: MCRL_wk0_ATD_p1_E05_AE


title: MCRL_wk0_ATD_p1_E02_AE


title: MCRL_wk0_ATD_p1_F03_AE


title: Motoneuron_P9A4


title: Motoneuron_P9B10


title: MCRL_wk0_ATD_p1_F09_AE


title: Motoneuron_P8G12


title: MCRL_wk0_ATD_p1_E10_AE


title: MCRL_wk0_ATD_p1_D10_AE


title: Motoneuron_P9A2


title: Motoneuron_P9B2


title: Motoneuron_P8G11


title: MCRL_wk0_ATD_p1_D06_AE


title: Motoneuron_P8G7


title: Motoneuron_P8G9


title: MCRL_wk0_ATD_p2_A08_AE


title: MCRL_wk0_ATD_p1_D07_AE


title: Motoneuron_P8G10


title: MCRL_wk0_ATD_p1_D03_AE


title: MCRL_wk0_ATD_p1_C10_AE


title: MCRL_wk0_ATD_p1_D08_AE


title: Motoneuron_P8F9


title: MCRL_wk0_ATD_p1_D05_AE


title: Motoneuron_P8F11


title: MCRL_wk0_ATD_p1_D02_AE


title: MCRL_wk0_ATD_p1_D01_AE


title: Motoneuron_P8F10


title: Motoneuron_P8F8


title: MCRL_wk0_ATD_p1_C07_AE


title: Motoneuron_P8F7


title: Motoneuron_P8G8


title: MCRL_wk0_ATD_p1_B09_AE


title: Motoneuron_P8F4


title: MCRL_wk0_ATD_p1_C06_AE


title: Motoneuron_P8F5


title: Motoneuron_P8G6


title: MCRL_wk0_ATD_p1_C04_AE


title: MCRL_wk0_ATD_p1_B10_AE


title: Motoneuron_P8F6


title: MCRL_wk0_ATD_p1_B06_AE