title: TLR4ΔIEC rep3 [TK_AP3]

city: 松江区

first: Mei

last: Qixiang

state: 上海市

address: 新松江路650号上海市第一人民医院

institute: 上海市第一人民医院

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm38.p5
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: intestinum

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: intestinum


title: TLR4ΔIEC rep2 [TK_AP2]

status: Public on Apr 26 2023

type: SRA

address: 新松江路650号上海市第一人民医院

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: age

tag: genotype

tag: tissue


title: TLR4ΔIEC rep1 [TK_AP1]

address: 新松江路650号上海市第一人民医院


title: WT rep3 [AP3]

address: 新松江路650号上海市第一人民医院

value: wild type


title: WT rep1 [AP1]

address: 新松江路650号上海市第一人民医院


title: WT rep2 [AP2]

address: 新松江路650号上海市第一人民医院


title: INPUT, ErfKO, 29, SR

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

library_source: genomic

data_processing:
read trimming: CUTADAPT (2.8)
alignment: bowtie 2 (2.3.5.1)
alignment processing: samtools (1.10)
peak calling: MACS2 (2.2.7.1)
idr_filtering: ChIPpeakAnno (3.26.4)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, bed/peaksets

molecule: genomic DNA

source_name: mouse trophoblast stem cells (mTSCs)

growth_protocol: Mouse TS cells were grown in a standard TS medium (RPMI 1640 supplemented with 20% fetal calf serum, 2mM L-Glutamine, 2mM sodium pyruvate and 100mM 2-mercaptoethanol) containing 70% mouse embryonic fibroblast -conditioned medium and 100 ng ml-1 Fgf2 and 1 µg ml-1 heparin. Cells were split every third day using trypsin.

extract_protocol:
ChIPseq libraries were generated with 5-10ng DNA using the NEBNext Ultra II DNA library preparation master mix (New England Biolabs, E7645) according to the manufacturer’s instructions.
RNAseq. RNA was extracted using RNeasy mini kit (Qiagen) and treated with DNaseI (Qiagen).
RNA-seq (Quantseq)

treatment_protocol: For differentiation, TSCs were exposed to 3 µM PD0325901 (Tocris) in full TSC media for 24h

tag: cell type

value: mouse trophoblast stem cells (mTSCs)

tag: differentiation state

value: self-renewal (SR)

tag: modification

value: ErfKO

tag: parental cell line

tag: chip antibody


title: INPUT, ErfKO, 2, PD

value: 24h differentiation with PD (PD)


title: INPUT, ErfKO, 29, PD


title: INPUT, Tbl1x, PD2

value: WT


title: INPUT, ErfKO, 2, SR


title: INPUT, Tbl1x, PD1


title: Tbl1x, ErfKO, 2, PD

description:
BIGWIGS.tar: Tbl1x_ErfKO_PD_163195_163197.bw
IDR_FILTERED.tar:  Tbl1x_ErfKO_PD_IDR_CPA.bed

value: anti-Tbl1x (Proteintech/13540-1-AP)


title: Tbl1x, ErfKO, 29, SR

description:
BIGWIGS.tar: Tbl1x_ErfKO_SR_163194_163196.bw
IDR_FILTERED.tar:  Tbl1x_ErfKO_SR_IDR_CPA.bed


title: Tbl1x, ErfKO, 29, PD


title: Tbl1x, ErfKO, 2, SR


title: INPUT, Tbl1x, SR2


title: INPUT, Tbl1x, SR1


title: Tbl1x, V5PD2

description:
BIGWIGS.tar: Tbl1x_V5PD_163192_163193.bw
IDR_FILTERED.tar:  Tbl1x_WT_PD_IDR_CPA.bed


title: Tbl1x, V5PD1


title: Tbl1x, V5SR2

description:
BIGWIGS.tar: Tbl1x_V5SR_163190_163191.bw
IDR_FILTERED.tar:  Tbl1x_WT_SR_IDR_CPA.bed


title: Tbl1x, V5SR1


title: G795-08 13 P

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

country: USA

institute: Penn State University

description: 13 P

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Dragen Host Software Version 01.011.588.3.7.5 allowing no mismatches in the index read. BBDuk (version 36_49) was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (GRCm38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. The reads were summarized to each gene using HTseq-count (version 0.11.2) by supplementing Ensembl gene annotation (GRCm38.78).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw read counts are provided in a G795_merged.HTSeq.out.csv.

source_name: proliferative zone in #13 mouse

extract_protocol:
RNA extraction was performed using the Picopure RNA Isolation Kit (Thermo Fisher Scientific). RNAs were amplified by two rounds of in vitro transcription using the Arcturus RiboAmp HS PLUS Kit (Thermo Fisher Scientific) according to the manufacturer’s protocols.
The cDNA libraries were prepared using the KAPA RNA HyperPrep Kit (Roche) as per the manufacturer's instructions. The unique dual barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing (NEXTFLEX® Unique Dual Index Barcodes, BioO Scientific). The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 57-65 cycles according to the manufacturer's instructions.

treatment_protocol: Axin2CreERT2;R26RTdTomato mice received three consecutive daily tamoxifen injections from P23 and sacrificed at P30. Sections of snap-frozen tibiae were prepared according to Kawamoto’s film method, as previously described (PMID: 25152035). Briefly, the adhesive surface of type 3c (16UF) (Section-lab) was attached to the specimen and 8-µm-thick sections were cut. Frozen specimens were immediately soaked in 80% ethanol for 30 s, then in 100% ethanol for 1 min (twice), then in xylene for 5 min at room temperature and subsequently they were dried for 5 min. The sections were subjected to laser microdissection (LMD) to collect TdTomato positive resting chondrocytes and unlabeled proliferative chondrocytes using a Leica LMD 7000 laser microdissection system (Leica Microsystems). Proliferative chondrocytes were defined by the location at least 50 μm away from secondary ossification cencer and the flattening moorphology.

tag: cell status

value: proliferative chondrocytes

tag: Sex

value: Female


title: embryonic hindlimb bud scRNA-seq

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

data_processing:
cellRanger (v2.2.0) was run on the raw data using the mm10 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: cellRanger filtered matrix; the provided mtx file contain a sparse matrix with genes on the rows and cells on the columns. The corresponding genes and cells identifiers are reported in files genes.tsv and barcodes.tsv, respectively.

molecule: polyA RNA

source_name: embryonic hindlimb bud

growth_protocol: Mice were maintained in animal facilties under standard conditions.

extract_protocol:
Microdissected hindlimb tissues were collected from 10 embryos at E10.5 (37-40 somites) in cold PBS. Tissues were dissociated to single cells using an enzymatic cocktail of Liberase and DNase I for 10 minutes at 37 degrees. Cells were passed through a 45 µm strainer to remove clumps and ensure a single cell suspension. Dead cells were eliminated with a ‘Dead Cell Removal Kit’ with magnetic beads (MACS, Milteny Biotech).
A single cell suspension of pooled live hindlimb cells were loaded into one well for single-cell capture using the Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics). Library preparation for each sample was also performed using the Chromium Single Cell 3’ Reagent Kit V2, and each sample was given a unique i7 index. Libraries were pooled and subjected to sequencing in an Illumina NovaSeq sequencer.

treatment_protocol: None.

value: embryonic hindlimb bud

tag: strain

value: Swiss Webster

tag: developmental stage

value: gestational day e10.5

tag: library type

value: Unstranded


title: G795-05 6 R

description: 6 R

source_name: resting zone in #6 mouse

value: resting chondrocytes


title: G795-04 2 P

description: 2 P

source_name: proliferative zone in #2 mouse

value: Male


title: G795-03 2 R

description: 2 R

source_name: resting zone in #2 mouse


title: G795-06 6 P

description: 6 P

source_name: proliferative zone in #6 mouse


title: G795-07 13 R

description: 13 R

source_name: resting zone in #13 mouse


title: G795-01 1 R

description: 1 R

source_name: resting zone in #1 mouse


title: heart, replicate 6, scRNAseq [p3_2]

city: 泸州

first: Xianhong

last: Ou

state: 四川

address: 四川省泸州市

department: Institute of Cardiovascular Research

institute: Southwest Medical University

description:
10x Genomics
p_barcodes.tsv.gz
p_features.tsv.gz
p_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat version 3.1.1 is used to single-celled quality control, analysis and data exploration
Assembly: mm10-1.2.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
E8.5 and E10.5 embryos were dissected from pregnant mice's uterus and digested with 0.25% trypsin after the cut-off in the head and limbs. The hearts from E12.5, E14.5, E16.5 and P3 stages were dissected directly from the embryos and postnatal mice, followed by the trypsin digestion. During the single-cell suspension preparation, cell viability and concentration were detected by staining with 0.4% trypan blue. After primary quality control, cell viability was adjusted to the appropriate concentration for 10×scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: heart

value: Wild-type C57Bl/6J


title: heart, replicate 5, scRNAseq [E16_5_2]

description: 10x Genomics


title: embryo, replicate 2, scRNAseq [E10_5_2]

description: 10x Genomics

source_name: embryo

value: embryo


title: heart, replicate 6, scRNAseq [p3_1]

description: 10x Genomics


title: heart, replicate 4, scRNAseq [E14_5_2]

description: 10x Genomics


title: heart, replicate 4, scRNAseq [E14_5_1]

description: 10x Genomics


title: heart, replicate 5, scRNAseq [E16_5_1_7F]

description:
10x Genomics
E16_5_1_barcodes.tsv.gz
E16_5_1_features.tsv.gz
E16_5_1_matrix.mtx.gz


title: heart, replicate 3, scRNAseq [E12_5_1]

description: 10x Genomics


title: heart, replicate 3, scRNAseq [E12_5_2]

description: 10x Genomics


title: heart, replicate 5, scRNAseq [E16_5_1_7]

description: 10x Genomics


title: embryo, replicate 1, scRNAseq [E8_5_2]

description: 10x Genomics


title: embryo, replicate 1, scRNAseq [E8_5_1]

description: 10x Genomics


title: 11H_M_3063

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 11H_M_3068


title: 11H_M_3066


title: 11H_M_3065


title: 11H_M_3064


title: 11H_M_3060


title: 11H_M_3059


title: 11H_M_3055


title: 11H_M_3056


title: 11H_M_3061


title: 11H_M_3057


title: 11H_M_3054


title: 11H_M_3058


title: 11H_M_3053


title: G795-02 1 P

description: 1 P

source_name: proliferative zone in #1 mouse


title: embryo, replicate 2, scRNAseq [E10_5_1]

description: 10x Genomics


title: 11H_M_3052


title: 11H_M_3051


title: 11H_M_3050


title: 11H_M_3048


title: 11H_M_3045


title: 11H_M_3047


title: 11H_M_3044


title: 11H_M_3042


title: 11H_M_3041


title: 11H_M_3067


title: 11H_M_3062


title: 11H_M_3039


title: 11H_M_3040


title: 11H_M_3036


title: 11H_M_3035


title: 11H_M_3033


title: 11H_M_3031


title: 11H_M_3030


title: 11H_M_3032


title: 11H_M_3029


title: 11H_M_3028


title: 11H_M_3025


title: 11H_M_3027


title: 11H_M_3024


title: 11H_M_3023


title: 11H_M_3022


title: 11H_M_3049


title: 11H_M_3021


title: 11H_M_3019


title: 11H_M_3020


title: 11H_M_3018


title: 11H_M_3017


title: 11H_M_3046


title: 11H_M_3016


title: 11H_M_3043


title: 11H_M_3015


title: 11H_M_3014


title: 11H_M_3013


title: 11H_M_3012


title: 11H_M_3011


title: 11H_M_3010


title: 11H_M_3037


title: 11H_M_3009


title: 11H_M_3034


title: 11H_M_3006


title: 11H_M_3004


title: 11H_M_3007


title: 11H_M_3005


title: 11H_M_3003


title: 11H_M_3001


title: 11H_M_3002


title: 11H_M_3000


title: 11H_M_3026


title: 11H_M_2999


title: 11H_M_2998


title: 11H_M_2996


title: 11H_M_2992


title: 11H_M_2993


title: 11H_M_2997


title: 11H_M_2991


title: 11H_M_2994


title: 11H_M_2990


title: 11H_M_2989


title: 11H_M_2987


title: 11H_M_2986


title: 11H_M_2982


title: 11H_M_2983


title: 11H_M_2981


title: 11H_M_2980


title: 11H_M_3008


title: 11H_M_2977


title: 11H_M_2979


title: 11H_M_2976


title: 11H_M_2978


title: 11H_M_2974


title: 11H_M_2971


title: 11H_M_2972


title: 11H_M_2969


title: 11H_M_2973


title: 11H_M_2970


title: 11H_M_2975


title: 11H_M_2968


title: 11H_M_2967


title: 11H_M_2966


title: 11H_M_2965


title: 11H_M_2964


title: 11H_M_2995


title: 11H_M_2963


title: 11H_M_2962


title: 11H_M_2988


title: 11H_M_2961


title: 11H_M_2960


title: 11H_M_2985


title: 11H_M_2984


title: 11H_M_2959


title: 11H_M_2957


title: 11H_M_2958


title: 11H_M_2954


title: 11H_M_2952


title: 11H_M_2951


title: 11H_M_2945


title: 11H_M_2948


title: 11H_M_2947


title: 11H_M_2944


title: 11H_M_2943


title: 11H_M_2942


title: 11H_M_2949


title: 11H_M_2940


title: 11H_M_2941


title: 11H_M_2937


title: 11H_M_2939


title: 11H_M_2935


title: 11H_M_2936


title: 11H_M_2938


title: 11H_M_2934


title: 11H_M_2933


title: 11H_M_2932


title: 11H_M_2931


title: 11H_M_2930


title: 11H_M_2927


title: 11H_M_2929


title: 11H_M_2926


title: 11H_M_2956


title: 11H_M_2924


title: 11H_M_2953


title: 11H_M_2955


title: 11H_M_2950


title: 11H_M_2923


title: 11H_M_2921


title: 11H_M_2919


title: 11H_M_2946


title: 11H_M_2922


title: 11H_M_2917


title: 11H_M_2918


title: 11H_M_2920


title: 11H_M_2916


title: 11H_M_2914


title: 11H_M_2910


title: 11H_M_2913


title: 11H_M_2915


title: 11H_M_2909


title: 11H_M_2906


title: 11H_M_2912


title: 11H_M_2905


title: 11H_M_2903


title: 11H_M_2904


title: 11H_M_2898


title: 11H_M_2901


title: 11H_M_2902


title: 11H_M_2897


title: 11H_M_2928


title: 11H_M_2894


title: 11H_M_2925


title: 11H_M_2893


title: 11H_M_2895


title: 11H_M_2892


title: 11H_M_2888


title: 11H_M_2891


title: 11H_M_2887


title: 11H_M_2889


title: 11H_M_2886


title: 11H_M_2890


title: 11H_M_2884


title: 11H_M_2883


title: 11H_M_2882


title: 11H_M_2911


title: 11H_M_2880


title: 11H_M_2881


title: 11H_M_2879


title: 11H_M_2878


title: 11H_M_2877


title: 11H_M_2812


title: 11H_M_2810


title: 11H_M_2811


title: 11H_M_2809


title: 11H_M_2808


title: 11H_M_2807


title: 11H_M_2896


title: 11H_M_2885


title: 11H_M_2787


title: 11H_M_2806


title: 11H_M_2803


title: 11H_M_2788


title: 11H_M_2801


title: 11H_M_2796


title: 11H_M_2793


title: 11H_M_2800


title: 11H_M_2798


title: 11H_M_2805


title: 11H_M_2790


title: 11H_M_2804


title: 11H_M_2802


title: 11H_M_2794


title: 11H_M_2795


title: 11H_M_2792


title: 11H_M_2786


title: 11H_M_2799


title: 11H_M_2791


title: 11H_M_2797


title: 11H_M_2789


title: 11H_M_2782


title: 11H_M_2778


title: 11H_M_2783


title: 11H_M_2779


title: 11H_M_2780


title: 11H_M_2784


title: 11H_M_2781


title: 11H_M_2777


title: 11H_M_2785


title: 11H_M_2772


title: 11H_M_2776


title: 11H_M_2773


title: 11H_M_2768


title: 11H_M_2766


title: 11H_M_2775


title: 11H_M_2769


title: 11H_M_2767


title: 11H_M_2759


title: 11H_M_2761


title: 11H_M_2764


title: 11H_M_2760


title: 11H_M_2771


title: 11H_M_2774


title: 11H_M_2765


title: 11H_M_2758


title: 11H_M_2757


title: 11H_M_2756


title: 11H_M_2755


title: 11H_M_2754


title: 11H_M_2750


title: 11H_M_2751


title: 11H_M_2749


title: 11H_M_2752


title: 11H_M_2753


title: 11H_M_2684


title: 11H_M_2681


title: 11H_M_2763


title: 11H_M_2762


title: 11H_M_2680


title: 11H_M_2678


title: 11H_M_2679


title: 11H_M_2676


title: 11H_M_2673


title: 11H_M_2670


title: 11H_M_2677


title: 11H_M_2669


title: 11H_M_2671


title: 11H_M_2675


title: 11H_M_2672


title: 11H_M_2682


title: 11H_M_2674


title: 11H_M_2770


title: 11H_M_2667


title: 11H_M_2668


title: 11H_M_2666


title: 11H_M_2665


title: 11H_M_2664


title: 11H_M_2683


title: 11H_M_2663


title: 11H_M_2662


title: 11H_M_2659


title: 11H_M_2660


title: 11H_M_2661


title: 11H_M_2658


title: 11H_M_2657


title: 11H_M_2656


title: 11H_M_2655


title: 11H_M_2654


title: 11H_M_2649


title: 11H_M_2648


title: 11H_M_2651


title: 11H_M_2650


title: 11H_M_2647


title: 11H_M_2643


title: 11H_M_2646


title: 11H_M_2645


title: 11H_M_2640


title: 11H_M_2641


title: 11H_M_2652


title: 11H_M_2653


title: 11H_M_2642


title: 11H_M_2644


title: 11H_M_2638


title: 11H_M_2637


title: 11H_M_2636


title: 11H_M_2634


title: 11H_M_2635


title: 11H_M_2632


title: 11H_M_2628


title: 11H_M_2629


title: 11H_M_2626


title: 11H_M_2627


title: 11H_M_2633


title: 11H_M_2631


title: 11H_M_2630


title: 11H_M_2639


title: 11H_M_2624


title: 11H_M_2622


title: 11H_M_2623


title: 11H_M_2299


title: 11H_M_2297


title: 11H_M_2295


title: 11H_M_2298


title: 11H_M_2625


title: 11H_M_2296


title: 11H_M_2293


title: 11H_M_2294


title: 11H_M_2292


title: 11H_M_2291


title: 11H_M_2290


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title: 11H_M_892


title: 11H_M_889


title: 11H_M_890


title: 11H_M_888


title: 11H_M_887


title: 11H_M_886


title: 11H_M_885


title: 11H_M_884


title: 11H_M_905


title: 11H_M_903


title: 11H_M_882


title: 11H_M_881


title: 11H_M_883


title: 11H_M_880


title: 11H_M_879


title: 11H_M_878


title: 11H_M_875


title: 11H_M_874


title: 11H_M_877


title: 11H_M_873


title: 11H_M_872


title: 11H_M_870


title: 11H_M_868


title: 11H_M_869


title: 11H_M_894


title: 11H_M_866


title: 11H_M_864


title: 11H_M_863


title: 11H_M_862


title: 11H_M_860


title: 11H_M_861


title: 11H_M_871


title: 11H_M_865


title: 11H_M_858


title: 11H_M_857


title: 11H_M_856


title: 11H_M_855


title: 11H_M_853


title: 11H_M_854


title: 11H_M_851


title: 11H_M_876


title: 11H_M_848


title: 11H_M_849


title: 11H_M_847


title: 11H_M_846


title: 11H_M_845


title: 11H_M_844


title: 11H_M_843


title: 11H_M_840


title: 11H_M_842


title: 11H_M_867


title: 11H_M_841


title: 11H_M_838


title: 11H_M_839


title: 11H_M_837


title: 11H_M_835


title: 11H_M_859


title: 11H_M_833


title: 11H_M_702


title: 11H_M_832


title: 11H_M_701


title: 11H_M_700


title: 11H_M_698


title: 11H_M_697


title: 11H_M_699


title: 11H_M_850


title: 11H_M_696


title: 11H_M_695


title: 11H_M_694


title: 11H_M_693


title: 11H_M_692


title: 11H_M_691


title: 11H_M_690


title: 11H_M_689


title: 11H_M_688


title: 11H_M_686


title: 11H_M_687


title: 11H_M_683


title: 11H_M_682


title: 11H_M_684


title: 11H_M_836


title: 11H_M_834


title: 11H_M_679


title: 11H_M_678


title: 11H_M_703


title: 11H_M_852


title: 11H_M_680


title: 11H_M_676


title: 11H_M_677


title: 11H_M_674


title: 11H_M_675


title: 11H_M_672


title: 11H_M_670


title: 11H_M_671


title: 11H_M_669


title: 11H_M_668


title: 11H_M_667


title: 11H_M_665


title: 11H_M_666


title: 11H_M_664


title: Testis REP1 (lanes 1-4)

city: Barcelona

first: luisa

last: santus

address: Plaça d'Eusebi Güell, 1-3

country: Spain

institute: Barcelona Supercomputing Center

data_processing:
We used Hisat v2.1.0 (Kim et al. 2019) to compute assembly indexes and known splice sites and mapped each samples’ reads to the assembly. We run Hisat2 with default parameters, except for rna-strandness, that we set to "FR", as inferred by InferExperiment.py from RSeQCc v3.0.0 (Wang et al. 2012)
We merged the lanes of each replicate (REP1 and REP2) with samtools -merge.
We removed duplicates with umi_tools dedup v1.0.0.
We excluded all samples with less than 10M sequenced reads, a mapping rate lower than 0.3 or a genic mapping rate lower than 0.7. We defined the genic mapping rate as the proportion of exonic and intronic reads, as computed by read_distribution.py from RSeQCc v3.0.0 (Wang et al. 2012).
We ran de novo transcriptome assembly separately on each sample with Stringtie v1.3.6 (Pertea et al. 2015), with default parameters except for strand information that was set to "--fr".
Genome_build: Mmul_10 (rheMac10)
Supplementary_files_format_and_content: Stringtie output: de novo transcriptome assembly in gtf format.
Supplementary_files_format_and_content: fpkm tpm

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Rhesus monkey total RNA was purchased from a vendor (Zyagen).
We prepared strand-specific RNA-Seq libraries using a dUTP-based method published previously (Levin JZ et al. Nat Methods 2010) with modifications. Starting from 100–1000 ng total RNA per sample, we performed ribosomal RNA depletion with antisense DNA oligos and RNase H (Matranga CB et al. Genome Biol 2014). During the cleanup of ribo-depleted RNA with RNAClean XP magnetic beads (Beckman Coulter), we eluted ribo-depleted RNA with 2X SuperScript IV Buffer and random hexamers (both Thermo Fisher Scientific) and fragmented the RNA at 94 °C for 3 min. We then added dNTPs, DTT, Superase-In RNase Inhibitor, actinomycin D to 0.2 µg/µL, and SSIV reverse transcriptase to 10 U/µL, incubated the reaction at room temperature for 10 min followed by slow ramping to 55 °C in an air incubator for 15 min, then 60 °C for 15 min, 65 °C for 15 min, and heat inactivation at 80 °C for 15 min. We performed second-strand synthesis with the Gubler-Hoffman method (aka nick translation; RNase H, DNA polymerase, and DNA ligase), with dUTP instead of dTTP to mark the second strand, at 16 °C for 2 h. Following cleanup on Ampure XP magnetic beads (Beckman Coulter), we treated cDNA with the NEBNext Ultra II End Repair/dA-Tailing Module (NEB) and then performed adaptor ligation with high-efficiency conditions detailed in SPRITE (Quinodoz SA et al. Cell 2018) at 20 °C for 1 h. To mark unique cDNA fragments, we ligated IDT xGen Dual Index UMI Adapters (MacConaill LE et al. BMC Genomics 2018), which include a random 9-mer unique molecular identifier (UMI) after the 8-bp i7 (Index 1) sample index. We then degraded the dUTP-marked second strand with Thermolabile USER II enzyme (NEB), purified the remaining first-strand cDNA on Ampure XP magnetic beads, and amplified each library with primers annealing to Illumina P5 and Illumina P7 sequences (IDT) with the NEBNext Ultra II Q5 Master Mix for 6–8 PCR cycles.

value: Testis

tag: disease state

value: healthy


title: 11H_M_663


title: 11H_M_662


title: 11H_M_685


title: 11H_M_661


title: Spleen REP1 (lanes 1-4)

source_name: Spleen

value: Spleen


title: SpinalCord REP2 (lanes 1-4)

source_name: Spinal Chord

value: Spinal Chord


title: Spleen REP2 (lanes 1-4)


title: 11H_M_659


title: 11H_M_681


title: 11H_M_658


title: LN REP1 (lanes 1-4)

source_name: Lymph Node

value: Lymph Node


title: LN REP2 (lanes 1-4)


title: Ovary REP1 (lanes 1-4)

source_name: Ovary

value: Ovary


title: Liver REP2 (lanes 1-4)

source_name: Liver

value: Liver


title: 11H_M_655


title: 11H_M_673


title: 11H_M_656


title: Kidney REP2 (lanes 1-4)

source_name: Kidney

value: Kidney


title: 11H_M_654


title: 11H_M_653


title: 11H_M_651


title: Kidney REP1 (lanes 1-4)


title: 11H_M_652


title: 11H_M_657


title: Brain REP1 (lanes 1-4)

source_name: Brain

value: Brain


title: Liver REP1 (lanes 1-4)


title: Skin REP2 (lanes 1-4)

source_name: Skin

value: Skin


title: 11H_M_660


title: 11H_M_646


title: 11H_M_648


title: 11H_M_650


title: 11H_M_649


title: Adrenal REP2 (lanes 1-4)

source_name: Adrenal gland

value: Adrenal gland


title: VeroCell76_SARSCOV2contaminated_scFTO_m6A-RIP_IP2_batch2

city: Bruxelles

first: Margot

last: CELERIER

address: 808 Route de Lennik

country: Belgium

institute: ULB

description: Ribo depleted total RNA

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to Chlorocebus sabaeus tRNA and rRNA sequences (Ensembl v101) with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
A built metagenome of both Chlorocebus sabaeus (Ensembl v100- ChlSab1.1.dna_sm.toplevel.fa.gz) and SARS-CoV-2 (NC_045512.2) reference genomes as extra chromosome has been created.Reads were then mapped against this metagenome using STAR algorithm (default parameters).
Coverage Bedgraph file were generated from map reads  using bamTobw with HPB normalization (https://github.com/YangLab/bamTobw)
Assembly: Chlorocebus sabaeus (Ensembl v100- ChlSab1.1.dna_sm.toplevel.fa.gz) and SARS-CoV-2 (NC_045512.2) reference genomes
Supplementary files format and content: Coverage Bedgraph file with HPB normalization

organism: Chlorocebus sabaeus

growth_protocol: Vero76 cells (african green monkey kidney, ATCC CRL-1587) were cultured in Dulbecco’s Modified Eagle Medium (Gibco, 41965-039) supplemented with 10% Fetal Bovine Serum (Gibco, 10270-106) and 1% penicillin/streptomycin (Gibco, 10378016) in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol:
(RNA purification) Total RNA was extracted with Trizol according to the manufacturer's instructions. Residual DNA removal was performed using Turbo DNase (ThermoFisher Scientific).  (m6A-immunoprecipitation) RNA was fragmented by mixing 90 µl RNA (at 0.9 µg/µl) and 10 µl fragmentation buffer 10X (100 mM Tris-HCl and 100 mM ZnCl2) in thin-walled 200-μl PCR tubes, then incubated at 94°C for 40 s in a pre-heated thermocycler block with the heated lid opened. 10 µl of 0.5 M EDTA was added and the tubes were placed on ice.  RNA was then subjected to sodium acetate precipitation and resuspended in 300 μl RNase-free water. RNA fragmentation size was assessed by running 0.25 µg RNA on a 2100 Bioanalyzer (Agilent) with the RNA Nano kit (Agilent). Furthermore, 2-5 µg of fragmented RNA was kept at -80°C to later serve as input control. The RNA was denatured by heating (70°C for 5 min, then put on ice) and the immunoprecipitation mix was prepared as follows: Fragmented RNA from cultured cells in 290 µl, 10µl proteinases inhibitors (Roche), 5 µl (200 units) RNasin® Ribonuclease Inhibitors (Promega), 5 µl of 200 mM Ribonucleoside Vanadyl Complex (RVC) (Sigma), 100 µl IP buffer 5X (50 mM Tris-HCl, 750 mM NaCl, 0.5% (vol/vol) Igepal), 3.5 µl anti-m6A antibody (Synaptic System, #202003) and 86.5 µl RNase-free water. The mix was incubated overnight at 4°C on a rotating wheel. The next day, 50 µl Dynabeads™ Protein G (Invitrogen, #10004D) were washed twice with IP buffer 1x supplemented with antiproteases (Roche) and blocked by incubating the beads in wash buffer supplemented with 0.5 mg/ml BSA for 1 h on a rotating wheel. The beads were washed again twice, then added to the immunoprecipitation mix and incubated for 2 h at 4°C on a rotating wheel. Then, the beads were washed three times with 1 ml washing buffer supplemented with 10 µl RNasin® and 10 µl RVC, and elution was performed by TriPure (Roche) extraction, so the RNA was resuspended in 9 µl RNase-free water.
The sequence library was prepared with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) for both input and IP samples.

treatment_protocol: Vero76 cells were inoculated with SARS-CoV-2 at an MOI of 0.001. For this, cells were incubated for 1h at 37°C and 5% CO2 with equal volume of diluted infectious stocks. Then, the virus-containing medium was removed, cells were washed twice with PBS and standard culture medium was added. Following 24h post inoculation, both culture supernatant and cells were harvested and subjected to RNA isolation

tag: batch

tag: technical replicates

value: replicate 2

tag: RNAi

value: Sc FTO

tag: rip antibody


title: VeroCell76_SARSCOV2contaminated_scFTO_m6A-RIP_INP_batch2

description: Ribo depleted total RNA

value: none (input)


title: Adrenal REP1 (lanes 1-4)

tag: tissue


title: VeroCell76_SARSCOV2contaminated_scFTO_m6A-RIP_IP1_batch2

description: Ribo depleted total RNA

value: replicate 1

tag: cell type

value: anti-m6A antibody (Synaptic System, #202003)


title: Chimpanzee_BA23_C2

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Chimp_Count_Matrix_snATACseq_Barcodes.txt
Chimp_Count_Matrix_snATACseq_Genes.txt
Chimp_Count_Matrix_snATACseq_MetaData.txt
Chimp_Count_Matrix_snATACseq.mtx
Seurat_Astrocyte_ATAC_Chimp.RDS
Seurat_Excitatory_ATAC_Chimp.RDS
Seurat_Inhibitory_ATAC_Chimp.RDS
Seurat_Microglia_ATAC_Chimp.RDS
Seurat_OPCOli_ATAC_Chimp.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger ATAC 1.1.0)
Supplementary_files_format_and_content: Read duplicates were removed (picard MarkDuplicates)
Peak calling (macs2 --nomodel, --keep-dup all, extsize 200, --shift –100 )
Common peak identification across samples and species (Refer to supplementary methods)
Peak-cell matrix generation (custom scripts)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed binarized peak-cell matrix: mtx file, peak and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

organism: Pan troglodytes

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol:
Nuclei for snATAC-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue as previously described: https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-6t8herw
Droplet-based single-nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library kit (1000110, 10x Genomics) according to the manufacturer’s protocols. Libraries were sequenced using an Illumina NovaSeq 6000.

value: brain

value: Brodmann Area 23

value: F

tag: age


title: 11H_M_647


title: 11H_M_645


title: VeroCell76_SARSCOV2contaminated_shFTO_m6A-RIP_IP2_batch2

description: Ribo depleted total RNA

value: Sh FTO


title: VeroCell76_SARSCOV2contaminated_shFTO_m6A-RIP_INP_batch2

description: Ribo depleted total RNA


title: VeroCell76_SARSCOV2contaminated_scFTO_m6A-RIP_IP2_batch1

description: Ribo depleted total RNA


title: 11H_M_643


title: Chimpanzee_BA23_C1

value: M


title: VeroCell76_SARSCOV2contaminated_shFTO_m6A-RIP_IP2_batch1

description: Ribo depleted total RNA


title: Brain REP2 (lanes 1-4)

value: healthy


title: VeroCell76_SARSCOV2contaminated_scFTO_m6A-RIP_IP1_batch1

description: Ribo depleted total RNA


title: VeroCell76_SARSCOV2contaminated_scFTO_m6A-RIP_INP_batch1

description: Ribo depleted total RNA


title: VeroCell76_SARSCOV2contaminated_shFTO_m6A-RIP_IP1_batch1

description: Ribo depleted total RNA


title: 11H_M_641


title: 11H_M_642


title: VeroCell76_SARSCOV2contaminated_shFTO_m6A-RIP_INP_batch1

description: Ribo depleted total RNA


title: hCiPSCs-0618 [scRNA]

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: 10x Genomics

data_processing:
The clean single-cell RNA-seq reads were mapped to human reference genome hg19 using Cell Ranger v3.1.0.
Assembly: hg19
Supplementary files format and content: .tar.gz files containing cellranger output

organism: Homo sapiens

extract_protocol:
Using single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, cells at different time points throughout chemical reprogramming process were harvested and resuspended at 1 x 106 cells per milliliter in 1 x PBS with 0.04% BSA. About 1 x 104 cells were added to each channel, and the target cell will be recovered was estimated to be about 5 x 103 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min, and hold at 4 ℃. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

tag: cell line

value: human chemically induced pluripotent stem cells


title: StageII-0618

description: 10x Genomics

library_source: genomic single cell

data_processing:
The single-cell ATAC-seq reads were mapped to human reference genome hg19 using Cell Ranger ATAC v1.2.0.
Assembly: hg19
Supplementary files format and content: gzipped .tsv files of cellrangerATAC output containing fragment data of each sample and its .tbi index file.

extract_protocol:
The nuclei were isolated and washed according to the method supplied by 10X Gemomis: Nuclei Isolation for Single Cell ATAC Sequencing (CG000169). Then the nucleus were resuspend by chilled Diluted Nuclei Buffer (10xGenomics; 2000153). The volume of Diluted Nuclei Buffer used to resuspend nuclei was based on the number of starting cells and the final target nuclei concentration. Countstar (Rigel S2) was used to count the nuclei. The nuclei were then immediately proceed to single cell ATAC-seq libraries.
Following the 10x Genomics single cell ATAC solution, by using Chromium Chip E Single Cell Kit(Product Code 1000156 ) and Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110), the nucleus in bulk sample are partitioned into nanoliter-scale Gel Beads-inemulsion (GEMs), a pool of ~750,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA of each individual nucleus, and libraries are generated (performed by CapitalBio Technology, Beijing). The libraries was sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25k read pairs per nucleus with pair-end 50 bp (PE50) reading strategy (performed by CapitalBio Technology, Beijing).

value: human somatic cells during chemical reprogramming stage II


title: RNA_Chimpanzee_BA23_C1

description:
All_Species_UMI_Count_Matrix_snRNAseq.mtx
All_Species_UMI_Count_Matrix_MetaData.txt
All_Species_UMI_Count_Matrix_Genes.txt
All_Species_UMI_Count_Matrix_Barcodes.txt
Seurat_Astrocyte_RNA.RDS
Seurat_Excitatory_RNA.RDS
Seurat_Inhibitory_RNA.RDS
Seurat_Microglia_RNA.RDS
Seurat_OPCOli_RNA.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger 3.1.0)
Chimpanzee, macaque reads were mapped to human (CrossMap)
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed expression matrix: mtx files, gene and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

extract_protocol:
Nuclei for snRNA-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.

tag: molecule subtype

value: nuclear RNA


title: 11H_M_639


title: 11H_M_640


title: StageIII_Day12-0618 [scRNA]

description: 10x Genomics

value: human somatic cells during chemical reprogramming stage III


title: StageIII_Day8-0618 [scRNA]

description: 10x Genomics


title: A80

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Nugen UniversalPlus

data_processing:
The raw sequencing reads were first trimmed with cutadapt to remove adaptor sequences, short sequences, and low quality bases (-m17, -q10, 17).
Trimmed reads were mapped to the 13-lined ground squirrel mitochondrial genome with hisat2 and remaining reads were mapped to transcript annotations on the HiC_Itri_2 genome (19) using Salmon (20) with -numBootstraps 50.
These Salmon assignments were imported into R, summarized by gene using tximport, and filtered to retain only genes with rlog-normalized counts of at least seven in at least 4/5 individuals from at least one group.
The counts were then transformed using rlog from the DESeq2 package and processed with limma’s removeBatchEffect to generate count tables corrected for library type.
Assembly: HiC_Itri_2 (https://www.ncbi.nlm.nih.gov/assembly/GCA_004006685.1; DOI: 10.3389/fphys.2020.624677)
Supplementary files format and content: csv file with batch-corrected rlog (log2) count matrix from DESeq2

organism: Ictidomys tridecemlineatus

source_name: Adrenal Gland

extract_protocol:
RNA extracted by homogenization with polytron in trizol, cleaned up with Direct-zol RNA MiniPrep Kit (Zymo Research)
Libraries were prepared using either the TruSeq Stranded mRNA Library Prep Kit (Illumina) or the Universal Plus mRNA Sequencing Kit (Nugen) as indicated in the sample metadata.

treatment_protocol: Animals implanted with temperature devices, kidney and adrenal gland tissue collected based on time and body temperature, flash frozen in LN2 immediately after dissection and kept continuously below -70C until RNA extraction.

value: Adrenal Gland

tag: hibernation state

value: SpD

tag: animal number


title: A79

description: Nugen UniversalPlus

tag: Sex


title: 11H_M_644

tag: strain


title: 11H_M_638


title: A171

description: Nugen UniversalPlus

value: IBA


title: VeroCell76_SARSCOV2contaminated_shFTO_m6A-RIP_IP1_batch2

description: Ribo depleted total RNA


title: A83

description: Nugen UniversalPlus


title: A165

description: Nugen UniversalPlus

value: Ar


title: A167

description: Nugen UniversalPlus

value: Ent


title: 11H_M_637


title: StageIII_Day6-0618 [scRNA]

description: 10x Genomics


title: A161

description: Nugen UniversalPlus


title: StageIII_Day4-0618 [scRNA]

description: 10x Genomics


title: A154

description: Nugen UniversalPlus


title: A141

description: Nugen UniversalPlus

value: SA


title: 11H_M_635


title: A155

description: Nugen UniversalPlus


title: 11H_M_636


title: StageIII_Day2-0618 [scRNA]

description: 10x Genomics


title: A139

description: Nugen UniversalPlus


title: StageIII_Day1-0618 [scRNA]

description: 10x Genomics


title: 11H_M_634


title: A138

description: Nugen UniversalPlus


title: A84

description: Nugen UniversalPlus


title: A137

description: Nugen UniversalPlus


title: StageIII_Day0.67-0618 [scRNA]

description: 10x Genomics


title: A130

description: Nugen UniversalPlus


title: 11H_M_633


title: A116

description: Nugen UniversalPlus

value: LAr


title: A115

description: Nugen UniversalPlus


title: 11H_M_632


title: StageIII_Day0.33-0618 [scRNA]

description: 10x Genomics


title: 11H_M_631


title: A111

description: Nugen UniversalPlus


title: A112

description: Nugen UniversalPlus


title: StageII_Day4-0618 [scRNA]

description: 10x Genomics


title: A104

description: Nugen UniversalPlus


title: 11H_M_630


title: StageII_Day8-0618 [scRNA]

description: 10x Genomics


title: A140

description: Nugen UniversalPlus


title: StageI_Day8-0618 [scRNA]

description: 10x Genomics

value: human somatic cells during chemical reprogramming stage I


title: 11H_M_629


title: A109

description: Nugen UniversalPlus


title: A9

description: Illumina TruSeq stranded


title: A7

description: Illumina TruSeq stranded


title: StageI_Day4-0618 [scRNA]

description: 10x Genomics


title: 11H_M_628


title: StageI_Day2-0618 [scRNA]

description: 10x Genomics


title: A8

description: Illumina TruSeq stranded


title: A5

description: Illumina TruSeq stranded


title: A4

description: Illumina TruSeq stranded


title: StageI_Day0.5-0618 [scRNA]

description: 10x Genomics


title: A6

description: Illumina TruSeq stranded


title: A3

description: Illumina TruSeq stranded


title: 11H_M_627


title: 11H_M_626


title: A2

description: Illumina TruSeq stranded


title: A1

description: Illumina TruSeq stranded


title: 11H_M_625


title: RNA_Chimpanzee_BA23_C3

value: brain

value: Brodmann Area 23


title: RNA_Chimpanzee_BA23_C4

value: F


title: 11H_M_623


title: 11H_M_624


title: RNA_Chimpanzee_BA23_C2


title: CPY-2_WES

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Central People's Hospital of Zhanjiang

data_processing:
FASTQC was used to measure the date quality of raw data in FASTQ format.
Reads passed QC were aligned to reference genome sequences using the BWA-MEM algorithm.
GATK HaplotypeCaller was used for germline variants calling.
Variants were filtered with a threshold of "DP >= 10.0 & GQ >= 30"
Assembly: hg38
Supplementary files format and content: VCF files containing germline variants passed QC for each sample, respectively.
Library strategy: Whole exome sequencing

source_name: peripheral blood mononuclear cells

extract_protocol:
The genomic DNA samples were extract from peripheral blood by using phenol-chloroform DNA isolation method.
The exome sequences were efficiently enriched from 0.4 μg genomic DNA using Agilent SureSelect Human All Exon V6 (Agilent, USA, Catalog #: 5190-8864) according tothe manufacturer's protocol. Firstly, genomic DNA was randomly fragmented to an average size of 180-280bp by Covaris S220 (Covaris, USA). Remaining overhangs were converted into blunt ends via exonuclease polymerase activities. Secondly, DNA fragments were end repaired and phosphorylated, followed by A-tailing and ligation at the 3' ends with paired-end adaptors. DNA fragments with ligated adapter molecules on both ends were selectively enriched in a PCR reaction. After PCR reaction, libraries hybridize with liquid phase with biotin labeled probe, then use magnetic beads with streptomycin to capture the exons of genes. Captured libraries were enriched in a PCR reaction to add index tags to prepare for sequencing. Products were purified using AMPure XP system (Beverly, USA), libraries were analyzed for size distribution by Agilent 5400 system (Agilent, USA )and quantified by QPCR (1.5 nM). The Qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

value: peripheral blood mononuclear cells

value: PBMCs

value: ciliopathy syndrome

tag: treatment


title: CPY-3_WES


title: Chimpanzee_BA23_C3

value: M


title: CPY-1_WES


title: Chimpanzee_BA23_C4


title: MM02-ME

city: Nanjing

first: Zhegnxu

last: Sun

address: Guangzhou Road 300

institute: Jiangsu Province Hospital

description: 10x Genomics

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.  Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.  Cell barcode and UMI were extracted. Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information. After that, we used STAR v2.6.1a  to map reads to the reference genome GRCh38 (ensembl version 92 annotation).  UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Further processing was done with Seurat v3.1.2 (quality control, dimension-reduction, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: myelomatous effusion

extract_protocol:
After using 40-micron sterile strainers to filter, the ascites sample were then centrifuged at 350× g for 5 min. Then the supernatant was discarded, and the sediment was resuspended in 1ml PBS (HyClone). Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells
Single-cell suspensiSingle-cell suspensions (200000 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.ons (200000 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: myelomatous effusion


title: MM02-BM

description: 10x Genomics

source_name: bone marrow

value: bone marrow


title: 11H_M_621

source_name: C57BL/6J Male P56 Mouse Brain


title: 11H_M_622


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 15

first: Collin

last: Joyce

state: California

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: 10x Genomics

data_processing:
BaseCall files were subsequently used to generate library-specific FASTQ files with cellranger mkfastq (v7.0.0) prior to running cellranger count (v7.0.0) with the GRCh38 (release 92) reference to produce cell barcode-gene expression matrices using default settings.
Assembly: GRCh38
Supplementary files format and content: Cellranger count output barcodes.tsv.gz, matrix.mtx.gz and features.tsv.gz files

source_name: Blood

extract_protocol:
Memory B cells separated from approximately 1x106 PBMCs by selective depletion (Switched memory B cell isolation kit; Miltenyi Biotec) were loaded according to the 10X Genomics manufacturer’s protocol for 5’-gene expression to attain 10,000 sequenced cells per well.
Gene expression libraries were prepared according to 10x genomics manufacturer’s protocol.

value: Blood

value: Memory B Cell


title: 55mpi,25-Jan-2013,V60,Non_Mem_GEX,biol rep 1

description: 10x Genomics

value: PBMC


title: CPY-4_WES


title: 55mpi,25-Jan-2013,V60,GEX,biol rep 2

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 13

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 14

description: 10x Genomics


title: 55mpi,25-Jan-2013,V60,GEX,biol rep 3

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 12

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 11

description: 10x Genomics


title: 11H_M_618


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 10

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 9

description: 10x Genomics


title: JS OMD

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

institute: ULiege

data_processing:
Raw data were demultiplexed into individual libraries. After filtering out reads mapping to rRNA, tRNA, mitochondrial RNA, and other contaminants (e.g., adapters, etc.) using bowtie2
Assembly: GRCh38
Supplementary files format and content: reads were aligned onto the human reference genome (GRCh38 and Ensembl 105 annotation) and quantified with Star to give the Counts file.

source_name: Bone

growth_protocol: Non-sclerotic trabecular bone was easily removed from the tibia with surgeon pliers and enzymatically processed to get digested bone pieces cultured. At confluence, osteoblasts were collected by trypsinization, seeded (22.000 cells/cm2) in 12-well plates (Nunc).

extract_protocol:
Total RNA was extracted from osteoblast cultures. Three well were pooled and cells were homogenized in 600 µl RTL lysis buffer (Qiagen) then extract using Rneasy mini kit from Qiagen according to the manufacturer's instructions. Dnase step were performed during extraction. Samples were eluted in 30 µl RNase free H2O. RNA quality indicator scores (RIN) was superior to 9.3.
0,1 µg of RNA from each culture condition was used for this analysis. Libraries were prepared with the Illumina Truseq stranded mRNA sample prep kit according to the manufacturer's instructions

treatment_protocol: Osteoblasts were cultured until confluence, then switched into differentiation media  (high glucose DMEM containing 2% UltroserG, 2mM glutamine, 50 µg/ml ascorbic acid and 20 µg/ml proline during 3 days, in the presence 10ng/ml of the human recombinant OMD (R&D systems, 2884-AD) or in its absence for the same patient, serving as its own control (CTRL).

value: Bone

value: Osteoblasts

tag: patient

value: JS

tag: time

tag: omd treatment


title: JX OMD

value: JX


title: JX CTRL


title: 11H_M_617

tag: brain region


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 6

description: 10x Genomics


title: 11H_M_616


title: JS CTRL


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 5

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 2

description: 10x Genomics


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 4

description: 10x Genomics


title: JO OMD

value: JO


title: 55mpi,25-Jan-2013,V60,GEX,biol rep 1

description: 10x Genomics


title: JO CTRL


title: 11H_M_620


title: 45mpi,03-Mar-2012,V48,Non_Mem_GEX,biol rep 1

description: 10x Genomics


title: 11H_M_615


title: 50mpi,10-Aug-2012,V54,GEX,biol rep 1

description: 10x Genomics


title: 11H_M_619


title: 11H_M_614


title: 11H_M_613


title: 45mpi,03-Mar-2012,V48,GEX,biol rep 3

description: 10x Genomics


title: 45mpi,03-Mar-2012,V48,GEX,biol rep 1

description: 10x Genomics


title: JM OMD

value: JM


title: 45mpi,03-Mar-2012,V48,GEX,biol rep 2

description: 10x Genomics


title: X68L_S53

first: Samuel

middle: Richard

last: Ward

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

data_processing:
quality control on raw fastq uisng FASTQC
aligned to rabbit genome
read quanitification using RSEM and Ensembl Orycun annotation
edgeR, limma-voom, followed by empirical bayes, TMM applied
design (Tenotomy - Sham)
Genome_build: Orycun2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryctolagus cuniculus

extract_protocol:
muscle was extracted and flash frozen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tenotomy, or a sham were performed(cut of the skin)

value: supraspinatus muscle

tag: time post-repair

tag: group


title: JK OMD

value: JK


title: X68R_S54

value: control


title: X66R_S50


title: X67L_S51


title: 11H_M_611


title: JK CTRL


title: X67R_S52


title: X66L_S49


title: JI OMD

value: JI


title: JI CTRL


title: X64L_S47


title: X64R_S48


title: X63R_S46


title: JG OMD

value: JG


title: 11H_M_609


title: 11H_M_607


title: X63L_S45


title: JM CTRL


title: X62R_S44


title: 11H_M_606


title: X62L_S43


title: X61R_S42


title: 11H_M_612


title: 11H_M_605


title: X61L_S41


title: X60L_S39


title: JE OMD

value: JE


title: JC OMD

value: JC


title: JE CTRL


title: 11H_M_610


title: 11H_M_604


title: X59L_S37


title: 11H_M_608


title: WRR_08_R_S64_R1_001


title: JC CTRL


title: 11H_M_603


title: JAG OMD

value: JAG


title: WRR_08_L_S63_R1_001


title: WRR_07_R_S62_R1_001


title: WRR_07_L_S61_R1_001


title: WRR_06_R_S60_R1_001


title: 11H_M_601


title: WRR_05_R_S58_R1_001


title: JAG CTRL


title: X60R_S40


title: JG CTRL


title: WRR_06_L_S59_R1_001


title: WRR_05_L_S57_R1_001


title: WRR_04_R_S56_R1_001


title: X59R_S38


title: WRR_04_L_S55_R1_001


title: JAC CTRL

value: JAC


title: WRR_03_R_S54_R1_001


title: 11H_M_598


title: WRR_03_L_S53_R1_001


title: JA OMD

value: JA


title: 11H_M_602


title: WRR_02_R_S52_R1_001


title: WRR_02_L_S51_R1_001


title: JA CTRL


title: WRR_01_R_S50_R1_001


title: 11H_M_597


title: WRR_01_L_S49_R1_001


title: 11H_M_596


title: 11H_M_595


title: 11H_M_594


title: 11H_M_600


title: 11H_M_593


title: JAC OMD


title: 11H_M_591


title: PSQ-0405Pre

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts derived with Subread:featureCount 1.46.p5.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCh38.76
Supplementary files format and content: The counts per million (CPM) reads were log-transformed (attached processed data file) and used to select genes that were significantly (P<0.005) positively and negatively associated with AT pO2 by using Pearson’s correlation.

source_name: muscle

growth_protocol: RNA was isolated from frozen skeletal muscle samples obtained from people  with obesity and prediabetes before and after 10% weight loss.

extract_protocol:
RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA)

value: Before


title: 11H_M_592


title: PSQ-0405Post

value: After


title: PSQ-0379Post


title: PSQ-0379Pre


title: PSQ-0343Pre


title: 11H_M_599


title: PSQ-0343Post


title: NejireHA_Nejire_cat_dead_rescue_rep3

city: Freiburg in Breisgau

first: Nicola

last: Iovino

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics

data_processing:
bcl-convert version 3.10.5 for data from 2022
bcl2fastq2 version 2.20.0.422 for data from 2021
hybrid reference genome is built using snakePipes-v2.5.2
trimming and mapping is done using DNA-mapping pipeline of snakePipes-v2.5.2
coverage files were generated using ChIP-seq pipeline of snakePipes-v2.5.2
Assembly: dm6
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: Stage 5 embryos

extract_protocol:
CUT&Tag experiments were performed as in Kaya-Okur, H.S., et al. 2019. Embryos were fixed with 1%PFA. 50 hand-staged embryos were used per sample. DNA was purified and 1pg of tagmented lambda phage genome was added to each sample as spike-in for quantification before library preparation.
Libraries were prepared by amplification of tagmented DNA fragments using NEBNext® Q5® HiFi PCR Master Mix (NEB, Cat. M0543). Primer sequences were taken from Buenrostro et al., 2015. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).

value: Stage 5 embryos

tag: genotype

value: NejireKD + Nejire catalytic dead rescue

tag: antibody

value: Anti-HA.11 Epitope Tag Antibody Covance

tag: assay

value: CUT&Tag

tag: spikein

value: lambda phage genome


title: NejireHA_Nejire_cat_dead_rescue_rep2

tag: tissue


title: NejireHA_Nejire_wt_rescue_rep3

value: NejireKD + Nejire wt rescue


title: 11H_M_590

tag: age


title: NejireHA_Nejire_cat_dead_rescue_rep1


title: PSQ-0320Post


title: PSQ-0266Pre


title: PSQ-0320Pre


title: 11H_M_587


title: NejireHA_Nejire_wt_rescue_rep1


title: NejireHA_Nejire_wt_rescue_rep2


title: 11H_M_589


title: Gcn5_Gcn5_wt_rescue_rep2

value: Gcn5KD + Gcn5 wt rescue

value: anti-Gcn5 homemade


title: PSQ-0266Post


title: Gcn5_Gcn5_cat_dead_rescue_rep1

value: Gcn5KD + Gcn5 catalytic dead rescue


title: Gcn5_Gcn5_wt_rescue_rep1


title: Gcn5_Gcn5_cat_dead_rescue_rep2


title: 11H_M_586


title: 11H_M_588


title: PSQ-0070Pre


title: 11H_M_584


title: PSQ-0070Post


title: Gcn5_wt_rescue_st5_rep3

description: 20211104_05_FRA_RNA_400x540_Gcn5Rescue_st5_rep3

data_processing:
Base-calling is done using bcl2fastq version: 2.20.0.422
for nuclear RNA data hybrid fastq reference is built using createIndices pipeline of snakePipes-v2.5.1
trimming and mapping is done using mRNA pipeline of snakePipes-v2.4.2
count matrices were built using mRNA pipeline of snakePipes-v2.4.2
differential analysis is done using mRNA pipeline of snakePipes-v2.4.2
Assembly: dm6
Supplementary files format and content: tsv (tab separated file)

extract_protocol:
For each biological replicate, 20 hand-sorted stage 2 or stage 5 embryos  were collected in 50μl of TRIzol™ (Thermo Fisher Scientific 15596026), homogenized with pestle and stored at -20°C. For nuclear RNAseq, nuclei pellets obtained from 300 stage 5 embryos were similarly collected and homogenized in 50μl of TRIzol™. RNA was then extracted in 500μl TRIzol mixed vigorously for 15 seconds with 100μl chloroform. For nuclear RNA-seq only, 1μl of 1:1000 diluted ERCC RNA spike-in (Ambion™ 4456740) was added with the remaining 450μl TRIzol before chloroform extraction, in order to normalize for a potential global variation of RNA quantity/nucleus upon knockdown. Samples were centrifuged at 12000g 4°C for 15min and the aqueous phase was mixed again with an equal volume of 300μl chloroform and centrifuged again at 12000g 4°C for 15min. The aqueous phase was mixed with 300μl of isopropanol and 20μg of glycogen and total RNA was let precipitate over night at -20°C. The day after, samples were centrifuged at 12000g 4°C for 30min and the RNA pellet was washed twice with 80% EtOH. Air dried RNA pellets were resuspended in 20μl of TURBO™ DNase solution (Invitrogen™ AM2238) and incubated for 30min at 37°C, according to manufacturer’s instructions. EDTA was added to a final concentration of 15mM and DNase was heat inactivated at 75°C for 10min.
Libraries were prepared by amplification of tagmented DNA fragments using NEBNext® Q5® HiFi PCR Master Mix (NEB, Cat. M0543). Primer sequences were taken from Buenrostro et al., 2015. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).


title: Gcn5_wt_rescue_st5_rep1

description: 20211104_01_FRA_RNA_400x540_Gcn5Rescue_st5_rep1


title: Gcn5_wt_rescue_st5_rep2

description: 20211104_03_FRA_RNA_400x540_Gcn5Rescue_st5_rep2


title: nuclearRNA_nejireKD_stage5_rep3

description: 20210615_06_FC_nuclearRNA_nejKD_emb_st5_rep3

molecule: nuclear RNA

value: NejireKD

tag: spike-in


title: Gcn5_cat_dead_rescue_st5_rep1

description: 20211104_02_FRA_RNA_400x541_Gcn5CatInactive_st5_rep1


title: Gcn5_cat_dead_rescue_st5_rep2

description: 20211104_04_FRA_RNA_400x541_Gcn5CatInactive_st5_rep2


title: 11H_M_583


title: PE-041Pre


title: PE-041Post


title: 11H_M_582


title: nuclearRNA_nejireKD_stage5_rep1

description: 20210615_04_FC_nuclearRNA_nejKD_emb_st5_rep1


title: PE-040Pre


title: nuclearRNA_control_stage5_rep3

description: 20210615_03_FC_nuclearRNA_WT_emb_st5_rep5

value: control


title: 11H_M_581


title: nuclearRNA_control_stage5_rep2

description: 20210615_02_FC_nuclearRNA_WT_emb_st5_rep2


title: PE-040Post


title: PE-035Pre


title: 11H_M_580


title: Nejire_cat_dead_rescue_st5_rep3

description: 20210820_24_FC_RNA_T6xN547_NEJKD-NEJDEADRESCUE_emb_st5_rep3


title: nuclearRNA_control_stage5_rep1

description: 20210615_01_FC_nuclearRNA_WT_emb_st5_rep1


title: Gcn5_cat_dead_rescue_st5_rep3

description: 20211104_06_FRA_RNA_400x541_Gcn5CatInactive_st5_rep3


title: 11H_M_585


title: 11H_M_579


title: Nejire_cat_dead_rescue_st5_rep1

description: 20210820_22_FC_RNA_T6xN547_NEJKD-NEJDEADRESCUE_emb_st5_rep1


title: Nejire_wt_rescue_st5_rep2

description: 20210820_20_FC_RNA_T6xN546_NEJKD-NEJWTRESCUE_emb_st5_rep2


title: PE-035Post


title: nuclearRNA_nejireKD_stage5_rep2

description: 20210615_05_FC_nuclearRNA_nejKD_emb_st5_rep2


title: Nejire_wt_rescue_st5_rep3

description: 20210820_21_FC_RNA_T6xN546_NEJKD-NEJWTRESCUE_emb_st5_rep3


title: PE-012Pre


title: Nejire_wt_rescue_st5_rep1

description: 20210820_19_FC_RNA_T6xN546_NEJKD-NEJWTRESCUE_emb_st5_rep1


title: HDAC6KD_batch1_stage2_rep2

description: 20200708_28_FC_RNA_T344xN174_HDAC6-KD_emb_st2_rep2

source_name: Stage 2 embryos

value: Stage 2 embryos


title: PE-011Pre


title: EnokKD_batch1_stage2_rep2

description: 20200708_24_FC_RNA_T337xN174_enok-KD_emb_st2_rep2

value: EnokKD


title: PE-012Post


title: HDAC6KD_batch1_stage2_rep1

description: 20200708_13_FC_RNA_T344xN174_HDAC6-KD_emb_st2_rep1


title: 11H_M_576


title: 11H_M_577


title: 11H_M_575


title: control_batch1_stage2_rep3

description:
Control for EnokKD and HDAC6KD
20200708_22_FC_RNA_T180xN174_CtrlAc-KD_emb_st2_rep2


title: EnokKD_batch1_stage2_rep1

description: 20200708_09_FC_RNA_T337xN174_enok-KD_emb_st2_rep1


title: control_batch1_stage2_rep2

description:
Control for EnokKD and HDAC6KD
20200708_15_FC_RNA_T180xN174_Ctrl-KD_emb_st2_rep2


title: PE-011Post


title: 11H_M_574


title: control_batch1_stage2_rep1

description:
Control for EnokKD and HDAC6KD
20200708_01_FC_RNA_T180xN174_Ctrl-KD_emb_st2_rep1


title: Nejire_cat_dead_rescue_st5_rep2

description: 20210820_23_FC_RNA_T6xN547_NEJKD-NEJDEADRESCUE_emb_st5_rep2


title: PE-007Post


title: PE-007Pre


title: 11H_M_578


title: HDAC1KD_stage2_rep3

description: 20201103_21_FC_RNA_T341xN174_HDAC1-KD_emb_st2_rep5


title: HDAC3KD_stage2_rep1

description: 20201103_25_FC_RNA_T103xN174_HDAC3-KD_emb_st2_rep3


title: PE-004Pre


title: HDAC1KD_stage2_rep2

description: 20201103_20_FC_RNA_T341xN174_HDAC1-KD_emb_st2_rep4


title: HDAC1KD_stage2_rep1

description: 20201103_19_FC_RNA_T341xN174_HDAC1-KD_emb_st2_rep3


title: 11H_M_571


title: 11H_M_570


title: PE-004Post


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 8

description: 10x Genomics

value: Blood

tag: cell type

value: Memory B Cell


title: Gcn5KD_stage2_rep3

description: 20201103_15_FC_RNA_T400xN174_Gcn5-KD_emb_st2_rep5


title: 11H_M_569


title: NejireKD_stage2_rep3

description: 20201103_09_FC_RNA_NI715xN174_nej-KD_emb_st2_rep5


title: Gcn5KD_stage2_rep1

description: 20201103_13_FC_RNA_T400xN174_Gcn5-KD_emb_st2_rep3


title: Gcn5KD_stage2_rep2

description: 20201103_14_FC_RNA_T400xN174_Gcn5-KD_emb_st2_rep4


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 7

description: 10x Genomics


title: 11H_M_568


title: NejireKD_stage2_rep2

description: 20201103_08_FC_RNA_NI715xN174_nej-KD_emb_st2_rep4


title: HDAC3KD_stage2_rep3

description: 20201103_27_FC_RNA_T103xN174_HDAC3-KD_emb_st2_rep5


title: NejireKD_stage2_rep1

description: 20201103_07_FC_RNA_NI715xN174_nej-KD_emb_st2_rep3


title: HDAC3KD_stage2_rep2

description: 20201103_26_FC_RNA_T103xN174_HDAC3-KD_emb_st2_rep4


title: 11H_M_573


title: 11H_M_567


title: 11H_M_572


title: control_stage2_rep3

description: 20201103_03_FC_RNA_T180xN174_Ctrl-KD_emb_st2_rep5


title: HDAC6KD_batch1_stage5_rep2

description: 20200708_58_FC_RNA_T344xN174_HDAC6-KD_emb_st5_rep2


title: control_stage2_rep2

description: 20201103_02_FC_RNA_T180xN174_Ctrl-KD_emb_st2_rep4


title: 11H_M_566


title: control_stage2_rep1

description: 20201103_01_FC_RNA_T180xN174_Ctrl-KD_emb_st2_rep3


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 5

description: 10x Genomics


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 4

description: 10x Genomics


title: 11H_M_565


title: EnokKD_batch1_stage5_rep2

description: 20200708_54_FC_RNA_T337xN174_enok-KD_emb_st5_rep2


title: HDAC6KD_batch1_stage5_rep1

description: 20200708_43_FC_RNA_T344xN174_HDAC6-KD_emb_st5_rep1


title: EnokKD_batch1_stage5_rep1

description: 20200708_39_FC_RNA_T337xN174_enok-KD_emb_st5_rep1


title: control_batch1_stage5_rep4

description: 20200708_45_FC_RNA_T180xN174_Ctrl-KD_emb_st5_rep2


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 2

description: 10x Genomics


title: control_batch1_stage5_rep3

description:
Control for EnokKD and HDAC6KD
20200708_52_FC_RNA_T180xN174_CtrlAc-KD_emb_st5_rep2


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 3

description: 10x Genomics


title: 11H_M_564


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 1

description: 10x Genomics


title: 11H_M_563


title: HDAC3KD_stage5_rep3

description: 20201103_30_FC_RNA_T103xN174_HDAC3-KD_emb_st5_rep5


title: 39mpi,16-Sep-2011,V42,GEX,biol rep 6

description: 10x Genomics


title: 34mpi,13-Apr-2011,V36,GEX,biol rep 7

description: 10x Genomics


title: control_batch1_stage5_rep2

description:
Control for EnokKD and HDAC6KD
20200708_37_FC_RNA_T180xN174_CtrlAc-KD_emb_st5_rep1


title: HDAC3KD_stage5_rep2

description: 20201103_29_FC_RNA_T103xN174_HDAC3-KD_emb_st5_rep4


title: 11H_M_562


title: HDAC3KD_stage5_rep1

description: 20201103_28_FC_RNA_T103xN174_HDAC3-KD_emb_st5_rep3


title: 34mpi,13-Apr-2011,V36,GEX,biol rep 6

description: 10x Genomics


title: 11H_M_560


title: HDAC1KD_stage5_rep1

description: 20201103_22_FC_RNA_T341xN174_HDAC1-KD_emb_st5_rep3


title: 34mpi,13-Apr-2011,V36,GEX,biol rep 4

description: 10x Genomics


title: Gcn5KD_stage5_rep2

description: 20201103_17_FC_RNA_T400xN174_Gcn5-KD_emb_st5_rep4


title: HDAC1KD_stage5_rep3

description: 20201103_24_FC_RNA_T341xN174_HDAC1-KD_emb_st5_rep5


title: 34mpi,13-Apr-2011,V36,GEX,biol rep 3

description: 10x Genomics


title: Gcn5KD_stage5_rep1

description: 20201103_16_FC_RNA_T400xN174_Gcn5-KD_emb_st5_rep3


title: 11H_M_558


title: HDAC1KD_stage5_rep2

description: 20201103_23_FC_RNA_T341xN174_HDAC1-KD_emb_st5_rep4


title: 34mpi,13-Apr-2011,V36,GEX,biol rep 2

description: 10x Genomics


title: NejireKD_stage5_rep3

description: 20201103_12_FC_RNA_NI715xN174_nej-KD_emb_st5_rep5


title: NejireKD_stage5_rep2

description: 20201103_11_FC_RNA_NI715xN174_nej-KD_emb_st5_rep4


title: control_stage5_rep3

description: 20201103_06_FC_RNA_T180xN174_Ctrl-KD_emb_st5_rep5


title: 11H_M_557


title: NejireKD_stage5_rep1

description: 20201103_10_FC_RNA_NI715xN174_nej-KD_emb_st5_rep3


title: control_stage5_rep2

description: 20201103_05_FC_RNA_T180xN174_Ctrl-KD_emb_st5_rep4


title: control_batch1_stage5_rep1

description:
Control for EnokKD and HDAC6KD
20200708_30_FC_RNA_T180xN174_Ctrl-KD_emb_st5_rep1


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 8

description: 10x Genomics


title: 34mpi,13-Apr-2011,V36,GEX,biol rep 1

description: 10x Genomics


title: 11H_M_556


title: 11H_M_555


title: 11H_M_554


title: 11H_M_561


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 6

description: 10x Genomics


title: H3K18ac_Nejire_cat_dead_rescue_rep2

data_processing:
Base-calling is done using bcl2fastq version: 2.20.0.422
hybrid reference genome is built using createIndices pipeline of snakePipes-v2.5.0
trimming and mapping is done using DNA-mapping pipeline of snakePipes-v2.5.1
coverage files were generated using ChIP-seq pipeline of snakePipes-v2.5.1
Assembly: dm6
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: Histone H3K18ac antibody (pAb) Active Motif


title: H3K18ac_Nejire_wt_rescue_rep3


title: H3K18ac_Nejire_cat_dead_rescue_rep1


title: H3K18ac_Nejire_cat_dead_rescue_rep3


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 7

description: 10x Genomics


title: H3K18ac_Nejire_wt_rescue_rep2


title: 11H_M_559

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 5

description: 10x Genomics


title: 11H_M_551


title: 11H_M_552


title: H3K9ac_Gcn5_cat_dead_rescue_rep2

value: H3K9ac - EpiCypher SNAP-ChIP


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 4

description: 10x Genomics


title: H3K9ac_Gcn5_cat_dead_rescue_rep1

value: Stage 5 embryos


title: 11H_M_550


title: H3K9ac_Gcn5_wt_rescue_rep1


title: H3K9ac_Gcn5_wt_rescue_rep2


title: H3K27ac_NejireKD_rep2

value: Anti-acetyl Histone H3(Lys27) (Clone No MABI0309) Wako


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 3

description: 10x Genomics


title: control_stage5_rep1

description: 20201103_04_FC_RNA_T180xN174_Ctrl-KD_emb_st5_rep3


title: H3K27ac_NejireKD_rep1


title: H3K27ac_wt_rep2


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 2

description: 10x Genomics


title: 11H_M_548


title: 11H_M_549


title: 28mpi,15-Oct-2010,V30,GEX,biol rep 1

description: 10x Genomics


title: H3K27ac_wt_rep1


title: 11H_M_547


title: H3K18ac_NejireKD_rep2


title: 23mpi,14-May-2010,V24,GEX,biol rep 8

description: 10x Genomics


title: H3K18ac_wt_rep1


title: 23mpi,14-May-2010,V24,GEX,biol rep 7

description: 10x Genomics


title: H3K18ac_NejireKD_rep1


title: 11H_M_545


title: 11H_M_546


title: 23mpi,14-May-2010,V24,GEX,biol rep 6

description: 10x Genomics


title: H3K9ac_Gcn5KD_rep2


title: H3K9ac_Gcn5KD_rep1


title: H3K18ac_Nejire_wt_rescue_rep1


title: 11H_M_544


title: 11H_M_543


title: H3K9ac_wt_rep2


title: H3K9ac_wt_rep1


title: 23mpi,14-May-2010,V24,GEX,biol rep 5

description: 10x Genomics


title: 11H_M_542


title: 23mpi,14-May-2010,V24,GEX,biol rep 4

description: 10x Genomics


title: H3K18ac_wt_rep2


title: 23mpi,14-May-2010,V24,GEX,biol rep 3

description: 10x Genomics


title: 11H_M_541


title: 23mpi,14-May-2010,V24,GEX,biol rep 2

description: 10x Genomics


title: 11H_M_540


title: 23mpi,14-May-2010,V24,GEX,biol rep 1

description: 10x Genomics


title: H9_H3K27me3_rep1

data_processing:
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was calculated using MACS2 while peak calling.
Assembly: hg19
Supplementary files format and content: .bw file containing merged signal intensity of each sample
Library strategy: CUT&TAG

extract_protocol:
Approximately 1 x 105 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol. Briefly, harvest fresh cultures and count 1 x 105 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4 oC. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 ℃ for 1 h and then performed DNA extraction with DNA extraction beads.
For extracted DNA, combinate i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and Illumina sequencing.

tag: cell line

value: hES cells H9


title: 11H_M_539

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain


title: H9_H3K27me3_rep2


title: H9_H3K4me3_rep1


title: H1_H3K27me3_rep1

value: hES cells H1


title: 20mpi,05-Feb-2010,V21,GEX,biol rep 5

description: 10x Genomics


title: 20mpi,05-Feb-2010,V21,GEX,biol rep 4

description: 10x Genomics


title: 160796E_2R-G-0-1

type: RNA

first: Yan

last: Zheng

address: 22 Zhongguancun South Avenue, Haidian District

institute: School and Hospital of Stomatology, Peking University

description: Gene expression data from human bone marrow-human mesenchymal stem cells before osteogenic induction

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner (G2565CA).

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label: biotin

source_name: human mesenchymal stem cells

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The  human mesenchymal stem cells were obtained from Cyagen Biosciences Inc., and the catalog number is HUXMA-01001. Cells were cultured in osteogenic media comprised DMEM with 10% FBS, 1% antibiotics, 100nM dexamethasone, 10mM β-glycerophosphate and 0.2 mM L-ascorbic acid.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: hMSCs cultured in the forth passage were inducing osteogenesis for different time period(0,7days).

value: human bone marrow

tag: treatment

value: before osteogenic induction


title: hCiPSCs-0809-1S#_H3K27me3_rep2

value: human chemically induced pluripotent stem cells


title: 160796D_R-G-7-2

description: Gene expression data from human bone marrow-human mesenchymal stem cells on the 7 days of osteogenic induction

value: 7 days of osteogenic induction


title: H1_H3K4me3_rep1


title: 160796D_R-G-7-1


title: 160796E_2R-G-0-2


title: H1_H3K4me3_rep2


title: 11H_M_537


title: 11H_M_538


title: H1_H3K27me3_rep2


title: 20mpi,05-Feb-2010,V21,GEX,biol rep 3

description: 10x Genomics


title: hCiPSCs-0809-1S#_H3K27me3_rep1


title: 20mpi,05-Feb-2010,V21,GEX,biol rep 2

description: 10x Genomics


title: H9_H3K4me3_rep2


title: hCiPSCs-0809-1S#_H3K4me3_rep1


title: hCiPSCs-0618-1S#_H3K27me3_rep2


title: 11H_M_535


title: hCiPSCs-0618-1S#_H3K27me3_rep1


title: hCiPSCs-0618-1S#_H3K4me3_rep2


title: 11H_M_534


title: 20mpi,05-Feb-2010,V21,GEX,biol rep 1

description: 10x Genomics


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 8

description: 10x Genomics


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 7

description: 10x Genomics


title: 11H_M_532


title: hCiPSCs-1013-1S#_H3K4me3_rep2


title: hCiPSCs-1013-1S#_H3K27me3_rep1


title: hCiPSCs-1013-1S#_H3K27me3_rep2


title: hADSCs-0809_H3K27me3_rep2

value: adult human adipose derived mesenchymal stromal cells


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 6

description: 10x Genomics


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 4

description: 10x Genomics


title: 11H_M_530


title: 11H_M_531


title: hADSCs-0809_H3K27me3_rep1


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 5

description: 10x Genomics


title: 11H_M_536


title: hCiPSCs-0809-1S#_H3K4me3_rep2


title: hADSCs-0809_H3K4me3_rep2


title: hADSCs-0809_H3K4me3_rep1


title: 11H_M_529


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 3

description: 10x Genomics


title: hADSCs-0618_H3K27me3_rep2


title: hADSCs-0618_H3K27me3_rep1


title: 11H_M_528


title: 11H_M_527


title: hADSCs-0618_H3K4me3_rep2


title: hADSCs-1013_H3K27me3_rep2


title: hCiPSCs-0618-1S#_H3K4me3_rep1


title: hADSCs-0618_H3K4me3_rep1


title: 11H_M_533


title: hCiPSCs-1013-1S#_H3K4me3_rep1


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 1

description: 10x Genomics


title: 11H_M_526


title: hADSCs-1013_H3K27me3_rep1


title: 11H_M_525


title: hADSCs-1013_H3K4me3_rep1


title: MM03-BM

description: GEXSCOPE

value: bone marrow


title: 14mpi,26-Aug-2009,V15,GEX,biol rep 3

description: 10x Genomics


title: 14mpi,26-Aug-2009,V15,GEX,biol rep 2

description: 10x Genomics


title: 11H_M_524


title: MM03-PB

description: GEXSCOPE

source_name: peripheral blood

value: peripheral blood


title: MM01-ME

description: GEXSCOPE

value: myelomatous effusion


title: 14mpi,26-Aug-2009,V15,GEX,biol rep 1

description: 10x Genomics


title: MM01-PB

description: GEXSCOPE


title: 11H_M_523


title: MM01-BM

description: GEXSCOPE


title: 11H_M_522


title: 17mpi,13-Nov-2009,V18,GEX,biol rep 2

description: 10x Genomics


title: Super-charged NK cells

city: West Allis

first: Ao

last: Mei

state: Wisconsin

address: 9442 West Maple Ct

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Natural killer cells are sorted from human PBMC as Lin-CD7+ population. Sorted cells are washed with ice-cold FACS buffer (PBS+10%FBS) and counted to be loaded into 10X Chromium machine.
scRNA libraries were prepared following the user guide of 10X Chromium Single Cell 3' Reagent Kits v3

value: Peripheral blood

tag: donor

value: healthy

value: Natural Killer cells

value: NK cells activated following the manuscript method