title: Patient 3, distal, scRNAseq

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive

institute: Duke University

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The doublets detecting was made using the Python package scrublet v0.2.3 (https://github.com/swolock/scrublet)
The cell filtering, annotation and sample integration were made using the R package Seurat v4.0.1 (https://satijalab.org/seurat)
The R package DropletUtils v1.10.3 was used to create a directory containing the filtered gene barcode matrix in the 10x format.
Assembly: mm10 (or hg38)
Supplementary files format and content: Tab-separated annotation files and matrix files

source_name: Lower extremity skeletal muscle

extract_protocol:
Skeletal muscle tissue was processed to generate single-cell suspensions using mechanical dissociation and enzymatic digestion. Live cells (PI- cells) were isolated by fluorescence-activated cell sorting using a SonySorter SH800s. For mouse HLI experiments, an equal number of PI- cells and PI-/CD31-/CD45- cells were pooled for each sample to increase the representation of relatively scarce non-hematopoietic and non-endothelial cell-types of interest (e.g. muscle stem cells and fibro-adipogenic progenitors). A total of approximately 150,000 cells were sorted for each sample, precisely counted using a hemocytometer, and used for scRNA-seq analysis.
Single-cell RNA sequencing libraries were generated using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s protocol. Approximately 16,000 - 24,000 cells per sample were used for GEM creation.

value: Lower extremity skeletal muscle cells

value: Lower extremity skeletal muscle

value: Chronic limb-threatening ischemia


title: 4-Cell_51h_51

status: Public on Oct 16 2023

type: SRA

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

library_source: genomic

data_processing:
Sequencing reads were aligned to the mm10 genome using bowtie2 (version 2.3.5) with the --local option. Duplicates were marked using samtools (version 1.9)and reads were filtered by keeping only properly paired reads, removing duplicates and selecting those whose mapping quality was higher or equal to 20. Bed files of the read coordinates were generated with bedtools (version 2.29.0) bamtobed command. Using bedtools intersect, read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM and then each bin by its respective average of all samples within the same stage, aiming to correct for the mappability biases intrinsic to the genomic regions. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.28.0) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 1.2.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
Assembly: mm10
Supplementary files format and content: tab-separated txt file with binary replication status
Library strategy: Single-cell Repli-seq

molecule: genomic DNA

organism: Mus musculus

source_name: 4-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. For the parthenogenetic embryos and IVF-derived zygotes, the timing of S-phase was calculated based on the time after activation and insemination, respectively. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment. For the Repli-seq with physically isolated pronuclei, we distinguished maternal and paternal pronucleus based on their size and their relative position to the second polar body and isolated either of them using micromanipulation. The remaining zygote containing a single pronucleus was also collected after removal of polar body so that both pronuclei from the same zygote were further processed for Repli-seq.
Individual blastomeres or pronuclei were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

treatment_protocol: For induction of parthenogenetic embryos, MII-stage oocytes were collected from superovulated females without mating. After removal of cumulus cells, oocytes were treated with 10 mM Sr2+ for 2 hours in Ca2+-free CZB medium and then incubated in KSOM. For generation of IVF-derived zygote, MII oocytes from F1 female mice (C57Bl/6J × CBA) were inseminated with activated spermatozoa obtained from the caudal epididymides of adult DBA/2J male mice. To inhibit both minor and major ZGA, embryos were treated with 0.1mg/mL a-amanitin from 17 hphCG injection until their collection time.

tag: tissue

value: 4-cell embryo

tag: genotype

value: (C57BL/6J x CBA) x DBA/2J

tag: treatment


title: 753_137_Lung - NaCl 56d - old

city: Biberach

first: Katrin

last: Fundel-Clemens

address: Birkendorfer 65

institute: Boehringer Ingelheim

library_source: transcriptomic

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using hg38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html).  Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences.   For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25 for human. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Assembly: GRCm38.86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: Lungs

extract_protocol:
A total of 20 mg of tissue was used for RNA isolation using the Qiazol kit according to manufacturer´s protocol (Qiagen, Hilden, Germany). Quality of RNA was assessed by the Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) using the SS RNA Kit (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries for RNA-seq were prepared using Tru-seq mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Bleomycin or saline administration was performed in a hanging position with a Vasofix-Braunüle 22G (B.Braun, Melsungen, Germany). Young mice received 0.7 mg/kg of Bleomycin sulphate (Merck, Darmstadt, Germany) and old mice 0.63 mg/kg.

value: Lungs

tag: disease state

value: Healthy

tag: age

value: old

value: NaCl

tag: day


title: 753_136_Lung - NaCl 56d - old


title: 4-Cell_51h_50


title: Spatial_transcriptomics_Day_0_Young

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: Loupe Browser (v5.0, 10x Genomics) was used to identify which spatial sequencing capture area spots were in contact with tissue. Demultiplexing and alignment was performed with Space Ranger (v2.1, 10x Genomics) and the mm10 2020-A reference transcriptome (10x Genomics).
Library strategy: Visium spatial RNA sequencing

source_name: Lung

extract_protocol: 10x Genomics

value: Lung

tag: strain

value: C57BL/6 mice

tag: timepoint

value: Day 0

tag: infection

value: Flu PR8 infection

tag: condition

value: Young


title: 4-Cell_51h_49


title: 753_142_Lung - Bleomycin 42d - old

value: Induced Pulmonary Fibrosis

value: Bleomycin


title: 753_135_Lung - NaCl 56d - old


title: Patient 2, distal, scRNAseq

department: Cell Biology

description: 10x Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

tag: cell type


title: Patient 3, proximal, scRNAseq

description: 10x Genomics


title: 4-Cell_50h_7


title: Spatial_transcriptomics_Day_0_Aged

value: Aged


title: Patient 1, distal, scRNAseq

description: 10x Genomics

value: Lower extremity skeletal muscle cells


title: 4-Cell_50h_6


title: Osteosarcoma SHH treatment 3 [U2OS SHH3]

city: Clayton

first: Vijesh

last: Vaghjiani

state: Victoria

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Reaserch

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
Forward and Reverse reads were aligned using RNA STAR on Galaxy and gene counts and Counts Per Million base obtained
Gene count tables were used to evaluate differentially expressed genes on Degust Platform at Monash University
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts and CPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts and CPM for every gene and every sample

source_name: Osteosarcoma

growth_protocol: MG63 and U2OS cell were grown in DMEM with 10% FBS in 6 well plates

extract_protocol:
RNA was extracted using Qiagen RNAeasy mini kit with DNAse I digest perfiormed on column
The samples were subjected to DNBSEQ eucaryotic strand-specific mRNA library preparation and paired end sequenced using DNBseq platform to a depth of 23 million reads per samples

treatment_protocol: Cells were treated with PBS or 1ug/ml rhSHH in serum free DMEM for 24 hours and RNA collected.

value: Bone

value: Osteosarcoma

tag: cell line

value: Immortalised cell line U2OS

value: SHH


title: 753_132_Lung - NaCl 56d - old

value: Lungs


title: Osteosarcoma SHH treatment 2 [U2OS SHH2]


title: Patient 2, proximal, scRNAseq

description: 10x Genomics

value: Lower extremity skeletal muscle

value: Chronic limb-threatening ischemia


title: 4-Cell_50h_4

value: 4-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: HPX_ZT14

type: RNA

city: Suita

first: Yoshiaki

last: Yamaguchi

state: Osaka

address: 3-3-35 Yamate-cho

department: Life Science and Biotechnology

country: Japan

institute: Kansai University

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on 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 Affymetrix Expression Console (Affymetrix) using RMA algorithm for normalization. For statistical analysis of the microarray data, we obtained values of 11 probes for the seminal proteins (Svs1, Svs2, Svs3a, Svs3b, Svs4, Svs5, Svs6, Sva, Sval1, Sval2, and Sval3) that were unlikely to be expressed in the SCN. We then subtracted the mean of 11 probes from the value of each gene assuming the mean value to represent zero expression.

label: biotin

source_name: HPX mouse SCN at ZT14

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 5.5 ug of fragmented cDNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Mice were reared in 12-h light/12-h dark condition.

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

value: Suprachiasmatic nucleus

value: HPX

tag: time point


title: Osteosarcoma SHH treatment 1 [U2OS SHH1]


title: 753_130_Lung - Bleomycin 42d - old

value: old


title: Osteosarcoma PBS control 3 [U2OS PBS 3]

value: PBS


title: 4-Cell_50h_8


title: 4-Cell_50h_3


title: 753_134_Lung - NaCl 56d - old

value: Healthy

value: NaCl


title: non-HPX_ZT14

source_name: non-HPX mouse SCN at ZT14

value: non-HPX


title: Patient 1, proximal, scRNAseq

description: 10x Genomics

value: Lower extremity skeletal muscle cells


title: 4-Cell_50h_2


title: Infected mouse 4, intravascular kidney B cells

city: Cambridge

first: Ondrej

last: Suchanek

address: Francis Crick Avenue

department: Department of Medicine, Molecular Immunity Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw MiSeq reads were filtered for base quality (median Phred score > 32) using QUASR 6.X.
Universal barcoded regions were identified in reads and orientated to read from V-primer to constant region primer. The barcoded region within each primer was identified and checked for conserved bases (i.e. the T’s in NNNNTNNNNTNNNNT). Primers and constant regions were trimmed from each sequence, and sequences were retained only if there was >80% sequence certainty between all sequences obtained with the same barcode, otherwise discarded. The constant region allele with highest sequence similarity was identified by 10-mer matching to the reference constant region genes from the IMGT database (v3.1.24), and sequences were trimmed to give only the region of the sequence corresponding to the variable (V–D–J) regions.
Isotype usage information for eachIghwas retained throughout the analysis hereafter. Sequences without complete reading frames and non-immunoglobulin sequences were removed and only reads with significant similarity to referenceIghvandIghjgenes from the IMGT database were retained using BLAST (v2.7.1).
Only sequences with more than one read were retained for further downstream analysis. IghvandIghjgenes and mutational status were determined for each BCR using IMGT/V-QUEST (v3.4.9).
Assembly: IMGT/V-QUEST (v3.4.9), reference for mouse IGH sequences (https://www.imgt.org/vquest/refseqh.html)
Supplementary files format and content: tab limited text files are  BLAST output and contain filtered (productive-only) nt BCR sequences with isotype information. These files were subsequently used as source (input) data for VDJ tools.
Supplementary files format and content: The processed txt files contain VDJ BCR sequences data based on alignment to IMGT/V-QUEST reference libraries for mouse IGH sequences (F+ORF+in-frame P) from this link https://www.imgt.org/vquest/refseqh.html
Library strategy: BCR-Seq

source_name: kidney

extract_protocol:
RNA was extracted from sorted B cell lysates using the RNeasy plus micro kit (QIAGEN) as per manufacturer’s instructions.
Reverse transcription (RT) was performed in two steps:  First, 1uL barcoded reverse primer mix (10uM per each primer), 1uL dNTP (10mM) and 14uL RNA template (up to 500ng) were mixed and heated to 65°C for 5 mins followed by an immediate transfer to ice for at least one minute. Second, mixture 2 including 4uL 5X First-Strand Buffer, 1uL DTT (0.1M), 1uL RNaseOUTTM (Thermo Scientific) and 1uL SuperScript®III (Life Technologies) was added and incubated at 50 °C for 60 min followed by 15 min inactivation at 70 °C. cDNA was cleaned-up with Agencourt AMPure XP beads and PCR amplified with V-gene multiplex primer mix (10 μM each forward primer) and 3′ universal reverse primer (10 μM) using KAPA protocol (KAPA Biosystems) and the thermal cycling conditions: 1 cycle (95 °C—5 min); 5 cycles (98 °C—5 s, 72 °C—2 min); 5 cycles (98°C—5 s, 65 °C—10 s, 72 °C—2 min); 30 cycles (98 °C—20 s, 60 °C—1 min, 72 °C—2 min) and 1 step (72 °C—7 min). Primers are provided in Supplementary Information (Table 1).

value: kidney

value: B cell

value: WT

value: UPEC


title: 753_128_Lung - Bleomycin 42d - old

value: Lungs

value: Induced Pulmonary Fibrosis

value: Bleomycin


title: Infected mouse 3, intravascular kidney B cells


title: 753_133_Lung - NaCl 56d - old


title: Osteosarcoma PBS control 2 [U2OS PBS 2]

value: Bone

value: Osteosarcoma

value: Immortalised cell line U2OS


title: Infected mouse 2, intravascular kidney B cells


title: 753_131_Lung - Bleomycin 28d - old


title: 4-Cell_50h_5

value: 4-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: Infected mouse 5, intravascular kidney B cells


title: Osteosarcoma PBS control 1 [U2OS PBS 1]

value: PBS


title: 4-Cell_50h_1


title: Osteosarcoma SHH treatment 3 [MG63 SHH3]

value: Immortalised cell line MG63

value: SHH


title: 753_126_Lung - Bleomycin 42d - old

value: old


title: 753_129_Lung - Bleomycin 42d - old


title: Control mouse 6, intravascular kidney B cells


title: 753_125_Lung - NaCl 42d - old

value: Healthy

value: NaCl


title: 2C_Ama_39h_56

source_name: 2-cell embryo + alpha-amanitin

value: 2-cell embryo + alpha-amanitin

value: alpha-amanitin


title: 753_124_Lung - NaCl 42d - old


title: Osteosarcoma SHH treatment 1 [MG63 SHH1]


title: HPX_ZT2

source_name: HPX mouse SCN at ZT2

value: Suprachiasmatic nucleus

value: HPX


title: 2C_Ama_39h_54


title: non-HPX_ZT2

source_name: non-HPX mouse SCN at ZT2

value: non-HPX


title: 2C_Ama_39h_53


title: 753_123_Lung - NaCl 42d - old

value: Lungs


title: Control mouse 5, intravascular kidney B cells

value: kidney

value: B cell

value: WT


title: 753_127_Lung - Bleomycin 28d - old

value: Induced Pulmonary Fibrosis

value: Bleomycin


title: Control mouse 3, intravascular kidney B cells

value: PBS


title: Osteosarcoma PBS control 3 [MG63 PBS 3]

value: Bone

value: Osteosarcoma

value: Immortalised cell line MG63


title: Osteosarcoma PBS control 2 [MG63 PBS 2]


title: 753_122_Lung - NaCl 42d - old

value: Healthy

value: old


title: Control mouse 2, intravascular kidney B cells


title: Infected mouse 1, intravascular kidney B cells

value: UPEC


title: 753_121_Lung - NaCl 42d - old

value: NaCl


title: Osteosarcoma PBS control 1 [MG63 PBS 1]


title: 2C_Ama_39h_52

value: 2-cell embryo + alpha-amanitin

value: (C57BL/6J x CBA) x DBA/2J

value: alpha-amanitin


title: 2C_Ama_39h_51


title: Control mouse 1, intravascular kidney B cells


title: 2C_Ama_39h_50


title: 2C_Ama_39h_55


title: 753_120_Lung - NaCl 42d - old

value: Lungs


title: Osteosarcoma SHH treatment 2 [MG63 SHH2]

value: SHH


title: Infected mouse 5, extravascular kidney B cells

value: kidney

value: B cell


title: 753_119_Lung - Bleomycin 35d - old

value: Induced Pulmonary Fibrosis


title: pool_size_experiment

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description:
dry seeds sorted to small, medium and large size from 4 biological replicas
pool_size

data_processing:
In our oligo(dT) primers two parts of UMI are split by barcode sequence, that is why we transformed read R1 fastq files using awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Read R2 of single seed libraries was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the count matrix for each seed from libraries and each gene was obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes and read R1 as well as a list of used barcodes as input. Count matrixes from different libraries were combined, seeds were renamed and used for further analysis using Seurat R package.
For seed sizes 3'RNA-seq analysis was performed as above expcept that subset of 32 oligo(dT) barcodes was used (see supplementary file). Count matrixes from different libraries were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

organism: Arabidopsis thaliana

source_name: seeds

growth_protocol: Dry after-ripened seeds stored at least 6 months before experiment.

extract_protocol:
For single seed analysis, 16 seeds were sparsely placed on a cooled glass microscopic slide and crashed using another glass microscopic slide. 2 ul of cold water was fast dropped on each seed debris on both slides. Matching two parts of each seed debris were mixed with water by pipetting and combined. 3 ul of seed extract was transferred to the PCR tube on ice. After all seeds were processed, 2 ul of digestion buffer (10 mM Tris-HCl pH 8.0, 1% Triton X-100, 1% Tween 20, 0.5 mM EDTA, 1.3 mg/ml proteinase K) and 1 ul of 10 mM barcoded oligo(dT) primer were added and mixed. Samples were incubated for 10 min at 65°C and 1 min at 85°C and placed on ice. For isolation of RNA from seed pools, frozen seeds were ground and mixed with 1 ml of homogenization buffer (100 mM Tris pH 9.5, 5 mM EDTA, 150 mM NaCl, 1 % sarkosyl, 0.5% b-mercaptoethanol). Seeds debris was centrifuged for 5 min 11,000g, the supernatant was transferred to fresh probe with 500 ul of chloroform and vortexed for 2 min. Then 500 ul of acid phenol was added and again vortexed for 2 min followed by centrifugation for 15 min 11,000g at 4°C. 900 ul of upper phase was transferred to a new tube and mixed with 90 ul of 3M sodium acetate and 600 ul of isopropanol. After 10 min incubation, RNA was pelleted by centrifugation for 15 min 11,000g at 4°C, the pellet was washed with 80% ethanol, dried and resuspended in 1ml of TRIzol. From that point, the procedure follows the standard protocol for RNA isolation with TRIzol.
For single seed libraries, digested extracts were mixed with 4 ul of reverse transcription mix (2 mM dNTPs, 2x SuperScriptIII reaction buffer, 10 mM DTT, 50 U of SuperScriptIII, 10 U of RiboLock), incubated for 30 min 42°C, 15 min 70°C and placed on ice. 32 cDNAs obtained using different barcoded oligo(dT) primers were pooled together, purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 3 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain 21 nt R1 (contain barcode and UMI) and 55 nt R2 (contain mRNA sequence). For transcriptomic analysis of seed pools, isolated RNA was treated with Turbo DNase (ThermoFisher) and 500 ng of it was used in reverse transcription using 50 mM different barcoded oligo(dT) primers and SuperScript III. 1/4 of each reaction was pooled and single library was prepared and sequenced exactly as above.

treatment_protocol: Secondary dormancy induction was performed by storing seeds on plates with water-soaked blue paper in 30°C in the dark for the indicated time. Seed recovery was performed by transferring these plates to constatnt light conditions for 24h.

tag: experiment type

value: seed pool analysis

value: seed

value: dry seeds

tag: size

value: multiplexed sample:small, medium and large


title: Control mouse 4, intravascular kidney B cells

value: WT

value: PBS


title: 753_118_Lung - Bleomycin 35d - old

value: old

value: Bleomycin


title: 2C_Ama_38h_72


title: Infected mouse 4, extravascular kidney B cells

value: UPEC


title: SD_L_7d24h_02

description:
7 days of secondary dormancy induction followed by 24h of recovery
sd_large_7d24h_2

value: single seed analysis

value: 7d SD induction + 24h recovery

value: large


title: SD_L_7d24h_01

description:
7 days of secondary dormancy induction followed by 24h of recovery
sd_large_7d24h_1


title: Infected mouse 3, extravascular kidney B cells


title: 2C_Ama_38h_71

value: 2-cell embryo + alpha-amanitin

value: (C57BL/6J x CBA) x DBA/2J

value: alpha-amanitin


title: 753_117_Lung - Bleomycin 35d - old

value: Lungs


title: Infected mouse 2, extravascular kidney B cells

value: kidney

value: B cell


title: 753_116_Lung - Bleomycin 35d - old

value: Induced Pulmonary Fibrosis


title: 2C_Ama_38h_70


title: Infected mouse 1, extravascular kidney B cells


title: Control mouse 6, extravascular kidney B cells


title: 2C_Ama_39h_49


title: 753_114_Lung - NaCl 35d - old

value: Healthy

value: NaCl


title: 753_115_Lung - NaCl 35d - old


title: 2C_Ama_38h_69


title: SD_S_7d24h_02

description:
7 days of secondary dormancy induction followed by 24h of recovery
sd_small_7d24h_2

value: seed

value: small


title: 2C_Ama_38h_67


title: SD_S_7d24h_03

description:
7 days of secondary dormancy induction followed by 24h of recovery
sd_small_7d24h_3


title: 753_113_Lung - NaCl 35d - old

value: old


title: SD_S_7d24h_01

description:
7 days of secondary dormancy induction followed by 24h of recovery
sd_small_7d24h_1


title: Control mouse 5, extravascular kidney B cells

value: WT

value: PBS


title: SD_L_7d24h_03

description:
7 days of secondary dormancy induction followed by 24h of recovery
sd_large_7d24h_3

value: single seed analysis


title: 2C_Ama_38h_66


title: Control mouse 4, extravascular kidney B cells


title: SD_L_3d_02

description:
3 days of secondary dormancy induction
sd_large_3d_2

value: 3d SD induction


title: SD_L_3d_03

description:
3 days of secondary dormancy induction
sd_large_3d_3

value: large


title: 2C_Ama_38h_65

value: 2-cell embryo + alpha-amanitin


title: 2C_Ama_38h_68

value: (C57BL/6J x CBA) x DBA/2J


title: 753_111_Lung - NaCl 35d - old


title: Control mouse 2, extravascular kidney B cells


title: 753_110_Lung - NaCl 35d - old


title: 2C_Ama_38h_48

value: alpha-amanitin


title: Control mouse 1, extravascular kidney B cells


title: 2C_Ama_38h_47


title: Control mouse 3, extravascular kidney B cells


title: 753_109_Lung - Bleomycin 28d - old

value: Lungs

value: Bleomycin


title: 753_108_Lung - Bleomycin 28d - old


title: 2C_Ama_38h_46


title: SD_S_3d_01

description:
3 days of secondary dormancy induction
sd_small_3d_1


title: SD_S_3d_02

description:
3 days of secondary dormancy induction
sd_small_3d_2


title: 753_107_Lung - Bleomycin 28d - old


title: Control LNA R2

city: Nijmegen

first: Ezio

last: Fok

state: Gelderland

address: Geert Grooteplein

department: Cell biology

country: Netherlands

institute: Radboud University

data_processing:
Seq2Science RNA-seq pipeline was used to process reads. Reads were trimmed using fastp, quantified with htseq and aligned to hg19 using the star aligner (min mapping quality 255). Differential gene expression was analyzed using DESeq2.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

growth_protocol: THP-1 cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% foetal bovine serum (FBS) (Gibco), GlutaMAX (Gibco) and Pen/Strep at 37˚C in a humidied incubator with 5% CO2

extract_protocol:
RNA was extracted using the Zymo RNA extraction kit according to the manufacturer's protocol
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit following the manufacturer’s protocol.

treatment_protocol: THP-1 cells were seeded with LNA and incubated for 24 hours. Cells were then stimulated with 10 ng/ml LPS for another 24 hours.

value: Monocyte

value: LPS


title: 2C_Ama_38h_45


title: ValLib_AssociationSeq

city: Muenster

first: Michael

middle: J

last: Ziller

address: Busso-Peus-Str. 10

institute: University of Muenster

description: ValLib_countMatrix_final_barcode_raw.txt

data_processing:
Associating MPRA barcodes with sequence elements: In order to associate the 3’ barcodes with its corresponding sequence/variant tested, we performed paired end sequencing of the intermediate MPRA library prior to inserting the minP-nanoLuc cassette, sequencing 150 cycles from either end on a Illumina MiSeq. Resulting FASTQ files were the modified to clip the 16bp barcode at the end of the second read to be included in the sequence name. Subsequently, the reads were aligned against a custom build reference of the original sequences included in each MPRA library using bwa version 0.7.17(Li and Durbin, 2009) in paired end mode. Resulting .bam files were converted to table format, only retaining aligned reads harboring the expected variant at the center position and including less than 5 clipped or mismatched bases. Subsequently, reads were collapsed onto individual barcodes and only barcodes covered by at least 2 reads and uniquely associated with one sequence element were retained for further analysis.
Processing of 3’ sequencing data: 3’mRNA sequencing data obtained from MPRA experiments in iPSC derived neurons or primary mouse cortical cultures were processed with a custom python scripts to count occurence of individual barcodes discovered in the data. All reads were filtered based on quality metrics, only retaining reads with less than 5 bases below a phred score of 20 and proper backbone sequence elements at the expected positions of the read, e.g. presence of the restriction site TCT and GAC. Subsequently, all 16mer barcodes from the remaining reads were counted initially, but only those barcodes also present in the quality-controlled results of the barcode-pEE association sequencing of the MPRA plasmid library were kept for quantitative analysis.
Assembly: hg19
Supplementary files format and content: table with the following columns: Barcode – unique 16mer barcode of mRNA fragment  Eid – unique Id of reference enhancer element that this barcode associates to  variantMapped – Boolean variable indicating if the expected SNP was detected at the correct position in the association sequencing  reference_name – name of the reference sequence fragment, corresponds to fasta file for this library  chrom – chromosome of enhancer fragment  chromstart – start coordinate of putative enhancer fragment  chromend – end coordinate of putative enhancer fragment  allele – detected allele in this fragment   ref_bases – reference allele for SNP that is interrogated by this putative enhance fragment  alt_bases – alternative allele for SNP that is interrogated by this putative enhance fragment  type – type of fragment, e.g. control or SNP   count – tag count of this fragment in the original plasmid library, used for normalization  followed by observed tag counts for MPRA all tag  count libraries from the different cell types and conditions evaluated

source_name: HEK

growth_protocol: iPSC derived neurons were generated via overexpression of pro-neural transcription factor Ngn2 plus small molecules and differentiated for 49 days on murine astrocytes. NPCs were differentiated based on the protocol from (Qi et al., 2017) with slight modifications. Primary mouse cortical cultures were generated from E15.5 mice cultured in vitro over a total of 12 days.

extract_protocol:
All cell types were directly lysed with lysis buffer (Quick-RNA Miniprep Kit, R1054, Zymogen). To increase the yield of the total RNA purification, QIAshredder columns (79654, Qiagen) were used before total RNA isolation. On-column DNAse digest was performed to digest DNA residues. Concentration of total RNA was measured by NanoDrop before performing mRNA isolation with the Poly(A)Purist MAG kit (AM1922, ThermoFisher Scientific) according to manufacturer’s protocol. Purification with glycogen was omitted and mRNA was directly isolated from the beads.
Association Seq: The fragments were amplified at the pMPRA1-enhancer-barcode stage in order to associate enhancer and their respective barcodes. The same forward primer (5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3’) was used for all amplifications, while the reverse primer (5’CAAGCAGAAGACGGCATACGAGAT NNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGTGCCAGAACATTTCTCTG3’) was barcoded (for barcode sequences see Table S7). 100 pg plasmid DNA, 1x Q5 Hot Start High-Fidelity 2x Master Mix (M0494L, NEB) and 0.5 µM reverse and forward primer were mixed and DNA was amplified at the following conditions: 98°C for 30 s, 16 cycles of [98°C for 10 s, 60°C for 30 s, 72°C for 20 s], and a final extension step for 2 min at 72°C. 8 PCR reactions were pooled and purified with Agencourt Ampure XP magnetic beads (A63881, Beckman Coulter) with a double sided selection with 0.55x and subsequently 0.35x of the volume of the pooled PCR product. Purification and clean-up were performed according to manufacturer’s recommendations. The correct fragment size and the concentration of the library were analyzed with the Bioanalyzer (High Sensitivity DNA Analysis, 5067-4626, Agilent). Library quantification was performed in triplicates with an RT-qPCR on the Illumina sequencing adapters according to manufacturer’s protocol (KAPA Library Quantification) on a Roche LightCycler® 480 System. 6-10 % PhiX were spiked into the final library of 6-10 pmol. Paired-end (150 bp each side) sequencing was performed with the MiSeq Reagent Kit (v2, 300-cycles, MS-102-2002, Illumina).  TagCountSeq: 30 µl mRNA were reverse transcribed into cDNA with 2 µl SuperScript IV reverse transcriptase (18090050, ThermoFisher Scientific) and 8 µl SuperScript™ IV VILO™ Master Mix (11756050, ThermoFisher Scientific): 25°C for 10 min, 50°C for 30 min and 85°C for 5 min. In order to analyze the activity of the enhancer, the barcodes were amplified from the cDNA: The PCR protocol described beforehand was used, but the cycle number was increased from 16 to 22 cycles. 0.5 µl cDNA were used for each of the 8 individual PCR reactions. The reverse primer was barcoded (barcode sequences Table S7). Sequence of primers: FW 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3’ and RV 5’CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttatcgacgagcgcctg3. As described above, PCR reactions were pooled and purified. Libraries were pooled equimolar according to their concentrations measured with the bioanalyzer.

treatment_protocol: Human iPSC derived glutamatergic iNeurons were infected during the splitting procedure on day 4. 1.5 - 4 µl MPRA-virus per million cells was added to the dislocated neurons for half an hour at RT. Cell differentiation proceeded then normally. NPCs were infected on day5 and then cultivated for another 3 days. 15-25 million neurons, 8 million NPCs, or 8 million primary neurons were infected per condition.

value: HEK

value: baseline


title: SD_L_3d_01

description:
3 days of secondary dormancy induction
sd_large_3d_1

value: seed


title: 753_112_Lung - NaCl 35d - old

value: Healthy

value: NaCl


title: AMANZI LNA KD R2

value: AMANZI KD


title: 753_106_Lung - NaCl 28d - old

value: old


title: AMANZI LNA KD R1


title: eqTLLib_AssociationSeq

description: eQTLLib_countMatrix_final_barcode_raw.txt


title: 2C_Ama_38h_43


title: DevLib_AssociationSeq

description: DevLib_countMatrix_final_barcode_raw.txt


title: 2C_Ama_38h_44


title: SD_S_3d_03

description:
3 days of secondary dormancy induction
sd_small_3d_3

value: single seed analysis

value: small


title: 2C_Ama_38h_42


title: snoRNA CD19_rep3

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

description:
healthy individual
total RNA

data_processing:
read adapter, quality and minimum length (15) trimming using Cutadapt.
Subsequent mapping to first rDNA precursor (https://www.ncbi.nlm.nih.gov/nuccore/555853), next tRNA (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/hg19-tRNAs.fa) with bowtie2 (version 2.2.5) to filter reads and finally to human genome hg38.
Mapped reads overlapping published snoRNAome regions (PMID: 27174936) were extracted, assigned by overlap and counted using the R environment for statistical computing using bioconductor packages GenomicAlignments and GenomicRanges. SnoRNA mapping profiles were manually inspected in order to ensure that we focus on high confidence full length snoRNA spanning reads with respect to their mapping position in the annotated snoRNA region. In case we found massive amount of reads which are either starting outside the expected 5’-region or inside the actual snoRNA region suggesting being a result of a fragmentation process, we established custom scripts to separate full length snoRNA reads from other. Read counts of other (not full length snoRNA) are provided in the count table as well.
Assembly: hg38
Supplementary files format and content: counts

source_name: CD19 enriched tissue

extract_protocol:
Multiple myeloma plasma cells were purified using CD138 (Miltenyi Biotech, Bergisch Gladbach, Germany). Total RNA was isolated with the AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. : 80224, Qiagen,  Hilden, Germany) according to the manufacturer’s manual. In case of healthy donors CD19+ B cells from peripheral blood were FACS sorted as control and RNA was extracted using the miRNeasy Kit (Cat. No. : 217084, Qiagen,  Hilden, Germany).
Libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina according to the instructions of the manufacturer.

value: CD19 enriched tissue


title: 753_104_Lung - NaCl 28d - old


title: Leaf protoplasts, total, biol rep 3

city: Vairao

first: Mariana

last: Sottomayor

state: Select:

address: Rua Padre Armando Quintas, No. 7

department: PLANTBIO

country: Portugal

institute: CIBIO, Research Centre in Biodiversity and Genetic Resources

data_processing:
Raw data was processed with Trimmomatic (version 0.39) with parameters: ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:50, to remove adaptors and low-quality bases, and to filter reads with ≤ 50 base pairs.
Data quality and statistics was verified using the FastQC tool (version 0.19.11).
Quantification was obtained following mapping with featureCounts (version 2.0.1, parameters: -p -t exon -g gene_id) against gene models of IDIO+.
Assembly: IDIO+ (supplementary file Catharanthus_transcriptome_IDIOplus.fasta ; accession number GKIJ00000000)
Supplementary files format and content: Tab-delimited text files include count values for each Sample

organism: Catharanthus roseus

source_name: leaf

growth_protocol: growth chamber, 25 ºC,  16/8 photoperiod, fluorescent light, medium intensity 70 μmol m-2s-0

extract_protocol:
Addition of  1% (v/v) ß-Mercaptoethanol in RLT buffer to cell suspensions with a volume ratio of 3.5:1, cell disruption by vortexing, RNA isolation with RNeasy Micro Kit (Qiagen). RNA precipitation with glycogen RNA-grade (Thermo Scientific).
Smart-seq2 kit

value: leaf

tag: developmental stage

value: fully developped leaves of flowering plants

value: total leaf protoplasts

tag: cultivar

value: Little Bright Eye

tag: protoplasts

value: Protoplasts were prepared as described in Carqueijeiro et al. 2016 Plant Physiol 171:2371-2378.


title: 2C_Ama_38h_41

tag: tissue

value: 2-cell embryo + alpha-amanitin

tag: genotype

value: (C57BL/6J x CBA) x DBA/2J

value: alpha-amanitin


title: snoRNA CD19_rep1

description:
healthy individual
total RNA


title: 753_103_Lung - NaCl 28d - old

value: Lungs

tag: disease state

tag: treatment


title: Control LNA R1

value: Monocyte

value: WT

value: LPS


title: snoRNA CD19_rep2

description:
healthy individual
total RNA


title: Leaf protoplasts, total, biol rep 2


title: 2C_Ama_38h_40


title: Leaf protoplasts, total, biol rep 1

growth_protocol: growth chamber, 25 ºC,  16/8 photoperiod, fluorescent light, medium intensity 70 μmol m-2s-


title: 2C_Ama_38h_39


title: 753_102_Lung - NaCl 28d - old

value: Healthy

tag: age

value: NaCl

tag: day


title: 753_101_Lung - Bleomycin 21d - old

value: Induced Pulmonary Fibrosis

value: old

value: Bleomycin


title: snoRNA T235

description:
newly diagnosed multiple myeloma
total RNA

source_name: CD138 enriched tissue

value: CD138 enriched tissue


title: snoRNA T234


title: snoRNA T233


title: 2C_Ama_38h_38


title: Leaf protoplasts, mesophyll, biol rep 2

value: leaf

value: fully developped leaves of flowering plants

value: mesophyll protoplasts

value: Protoplasts were prepared and sorted by FACS as described in Carqueijeiro et al. 2016 Plant Physiol 171:2371-2378.


title: 2C_Ama_38h_37

value: 2-cell embryo + alpha-amanitin


title: 753_100_Lung - Bleomycin 21d - old


title: Leaf protoplasts, mesophyll, biol rep 1

value: Little Bright Eye


title: Leaf protoplasts, mesophyll, biol rep 3


title: 753_098_Lung - Bleomycin 21d - old


title: snoRNA T231


title: 2C_Ama_38h_36

value: (C57BL/6J x CBA) x DBA/2J

value: alpha-amanitin


title: Leaves, biol rep 2

extract_protocol:
RNeasy Plant Mini Kit (Qiagen)
Smart-seq2 kit

value: whole leaves

value: not applicable


title: snoRNA T230


title: Leaves, biol rep 1


title: 753_105_Lung - NaCl 28d - old

value: Lungs


title: 753_096_Lung - Bleomycin 21d - old


title: 753_097_Lung - Bleomycin 21d - old


title: 2C_Ama_38h_35


title: snoRNA T229


title: snoRNA T228


title: 2C_Ama_38h_34


title: Leaves, pair 4, outdoors, biol rep 3

growth_protocol: outdoors, south oriented location

extract_protocol:
RNeasy Plant Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit

value: fourth leaf pair from apex of fowering plants


title: 2C_Ama_38h_33


title: 753_099_Lung - Bleomycin 21d - old


title: 753_095_Lung - NaCl 21d - old

value: Healthy

value: NaCl


title: Leaves, pair 4, outdoors, biol rep 2


title: Leaves, pair 4, outdoors, biol rep 1


title: 2C_Ama_37h_31


title: 753_093_Lung - NaCl 21d - old

value: old


title: 753_094_Lung - NaCl 21d - old


title: Leaves, pair 4, indoors, biol rep 2

growth_protocol: growth chamber, 25 ºC,  16/8 photoperiod, fluorescent light, medium intensity 70 μmol m-2s-7


title: 2C_Ama_37h_32


title: snoRNA T227


title: 753_092_Lung - NaCl 21d - old


title: Leaves, pair 4, indoors, biol rep 3


title: snoRNA T225


title: 2C_Ama_37h_30


title: 2C_Ama_37h_29


title: snoRNA T226


title: 753_091_Lung - NaCl 21d - old


title: snoRNA T223


title: Leaves, pair 4, indoors, biol rep 1

growth_protocol: growth chamber, 25 ºC,  16/8 photoperiod, fluorescent light, medium intensity 70 μmol m-2s-22


title: 2C_Ama_37h_28


title: 753_090_Lung - NaCl 21d - old


title: snoRNA T222


title: snoRNA T221


title: Leaves, pair 1, outdoors, biol rep 3

value: first leaf pair from apex of fowering plants


title: 2C_Ama_37h_26


title: 753_088_Lung - Bleomycin 14d - old

value: Induced Pulmonary Fibrosis

value: Bleomycin


title: 2C_Ama_37h_27


title: Leaves, pair 1, outdoors, biol rep 2

value: leaf


title: Leaves, pair 1, outdoors, biol rep 1


title: snoRNA T219

value: CD138 enriched tissue


title: 2C_Ama_37h_25


title: snoRNA T217


title: Leaves, pair 1, indoors, biol rep 3


title: 753_087_Lung - Bleomycin 14d - old


title: snoRNA T224


title: Leaves, pair 1, indoors, biol rep 2


title: 2C_Ama_36h_9


title: 753_086_Lung - Bleomycin 14d - old


title: snoRNA T212


title: 2C_Ama_36h_24


title: Leaves, pair 1, indoors, biol rep 1


title: snoRNA T210


title: snoRNA T211


title: 753_085_Lung - Bleomycin 14d - old


title: 2C_Ama_36h_22


title: 753_089_Lung - Bleomycin 14d - old


title: Leaf protoplasts, idioblasts, biol rep 3

value: fully developped leaves of flowering plants

value: idioblast protoplasts

value: Protoplasts were prepared and sorted by FACS as described in Carqueijeiro et al. 2016 Plant Physiol 171:2371-2378.


title: 2C_Ama_36h_23

value: 2-cell embryo + alpha-amanitin

value: (C57BL/6J x CBA) x DBA/2J


title: 753_084_Lung - Bleomycin 14d - old


title: 753_083_Lung - NaCl 14d - old


title: snoRNA T206


title: Leaf protoplasts, idioblasts, biol rep 1

value: Little Bright Eye


title: 753_082_Lung - NaCl 14d - old


title: 2C_Ama_36h_21

value: alpha-amanitin


title: Leaf protoplasts, idioblasts, biol rep 2


title: 2C_Ama_36h_20


title: 753_081_Lung - NaCl 14d - old

value: Lungs


title: Cereblon_Overexpression, scRNA-seq

city: St Louis

first: Laurence

middle: A.

last: Lemaire

state: MO

address: 3507 Laclede Ave

department: Biology

institute: Saint Louis University

description: Single cell RNA sequencing from Ciona mid tailbud embryos expressing in the tail muscle GFP targeted to the membrane and Cereblon (Crbn)

data_processing:
Filtering, quality control of the raw sequencing and generation of the FASTQ files were performed as described by Cao and colleagues in 2019. Briefly, the raw sequencing reads were filtered by Illumina NovaSeq Control Software. Reads aligning to phix using Bowtie version 1.1.1 and those falling the default chastity filter of Illumina were removed. To separate control and Crbn overexpression conditions, the reads were demultiplexed using barcode_splitter version 0.18.2, allowing one mismatch in the barcode.
To generate the gene barcode matrices, the FASTQ files were processed with 10x Cell Ranger version 3.0.0.
Assembly: Ciona intestinalis type A KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/download_kh.html)
Supplementary files format and content: gene barcode matrices

organism: Ciona intestinalis

source_name: Ciona intestinalis type A

growth_protocol: Gametes from Ciona intestinalis type A were collected as described by Christians and Collegeagues in 2009. Fertilized eggs were electroporated (see treatment protocol) and grow until the mid tailbud stage.

extract_protocol:
Mid tailbud embryos were dissociated into single cells using trypsin in sea water following the protocol published by Cao and colleagues in 2019.
Between 1000 and 2000 cells per condition were loaded onto the Chromium Controller (10x Genomics). The cells were lysed, the polyA RNA was retro-transcribed, barcoded with the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics) using the protocols provided by the manufacturer. Nextera DNA library prep kit (Illumina) was used to construct Illumina sequencing libraries from amplified cDNA. The libraries were then sequenced on a Illumina NovaSeq 6000 instruments with the SP reagent kit (100 cycles, paired-end).

treatment_protocol: Fertilized eggs were electroporated with either plasmids coding for a membrane GFP expressed in the tail muscle (Tbx6b>T2A-GFPCAAX, control condition) or plasmids coding for Cereblon and a membrane GFP expressed in the same tissue (Tbx6b>Crbn-T2AGFPCAAX, Crbn overexpression condition). Once the fluorescence could be detected, morphologically heathly GFP+ embryos were selected.

value: Mid tailbud embryo


title: 753_080_Lung - NaCl 14d - old

value: Healthy


title: 2C_Ama_36h_19


title: Cereblon_Control, scRNA-seq

description: Single cell RNA sequencing from Ciona mid tailbud embryos expressing in the tail muscle GFP targeted to the membrane


title: snoRNA T200


title: snoRNA T201


title: snoRNA T198


title: 753_079_Lung - NaCl 14d - old

value: NaCl


title: 2C_Ama_36h_18


title: 753_078_Lung - NaCl 14d - old

value: old


title: human_skin_3

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

country: China

institute: Zhejiang University

description: 10x Genomics

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)
The analysis was performed with R package Seurat 5.0
The data sets were integrated in to one, the single nuclei with over 50 genes were used for analysis, cells were clustered at resolution of 0.5. Uniform manifold approximation and projection (UMAP) was used to reduce the data dimensionality to visualize single-nucleus data.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include baseMean for each gene

source_name: skin

extract_protocol:
Single nuclei were isolated with Minute Single Nucleus Isolation Kit for Tissues/Cells (Invent Biotechnologies, Inc, Minnesota). The tissue was minced into pieces and lysed in cold lysis buffer, lysate was filtered with centrifuge filter, cell pellet was resuspended in PBS containing 5% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
single cell 3’ v3 protocol, 10x Genomics

treatment_protocol: All ticks were removed from the skin with forceps and the bite sites were biopsied under sterile conditions using a 3 mm punch immediately after removal of the tick.

value: skin


title: 2C_Ama_36h_17


title: snoRNA T197


title: 753_077_Lung - None 0d - old


title: snoRNA T195


title: human_skin_1

description: 10x Genomics


title: human_skin_2

description: 10x Genomics


title: snoRNA T202


title: 2C_Ama_36h_16


title: 753_076_Lung - None 0d - old


title: 2C_Ama_36h_14


title: 2C_Ama_36h_15


title: 753_075_Lung - None 0d - old


title: snoRNA T194


title: RH4, H3K27ac, HiChIP

city: Rome

first: Matteo

last: Cassandri

address: Viale di San Paolo 15

department: Department of Oncohematology

country: Italy

institute: Bambino Gesù Children's Hospital

data_processing:
HiChIP reads were aligned to the human (hg38) or mouse (mm10) reference genome using Bowtie2.
Downstream analysis was performed following HiC-Pro pipeline (Servant et al. 2015).
HiChIP-reads were filtered for read pairs with contact range >1000bp.
Assembly: hg38
Supplementary files format and content: hic files are provided at chromosome level.
Library strategy: HiChIP

growth_protocol: RD and RH4 cells were cultured in DMEM high-glucose (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% penicillin-streptomycin. All the cell lines were cultured at 37°C in a humidified atmosphere of 5% CO2/ 95% air and regularly checked for mycoplasma contamination.

extract_protocol:
HiChIP was performed using the Dovetail MNase-HiChIP kit (#21007, Dovetail Genomics) following manufacturer’s instruction. 10x10^6 RD FN-RMS and RH4 FP-RMS cells were collected and snap-frozen at -80C for at least 30 minutes. Cells were then crosslinked with disuccinimidyl glutarate (DSG, #A35392, Thermo Fisher) and 37% formaldehyde. Chromatin lysates extracted from C2C12 mouse cells were used as spike-in for AQuA-normalization and chromatin immunoprecipitation of H3K27ac (MABE647, Millipore) was performed overnight.
HiChIP libraries were prepared using the Dovetail MNase-HiChIP kit following manifacturer's instruction.

value: Fusion-Positive Rhabdomyosarcoma

value: WT

tag: chip-antibody

value: H3K27ac (Millipore, MABE674)


title: RD, H3K27ac, HiChIP

source_name: RD

value: RD

value: Fusion-Negative Rhabdomyosarcoma


title: snoRNA T190

value: CD138 enriched tissue


title: 753_074_Lung - None 0d - old

source_name: Lungs


title: 2C_Ama_36h_13


title: snoRNA T186


title: 2C_Ama_36h_12


title: shDDP3

city: Beijing

first: Xiaoyang

last: Han

address: Qihelou

department: Beijing Obstetrics and Gynecology Hospital

institute: Capital Medical University

data_processing:
Data filter
Comparative analysis
Expression analysis
Enrichment analysis
Assembly: GRCh38.100.chr
Supplementary files format and content: fpkm

extract_protocol:
RNA was extracted using Trizol method. Total RNA with nuclease free water to final volume of 50µl is used for construction of sequencing library.
Using the fragmented RNA as a template, a random primer was used for reverse transcription to achieve the synthesis of the first strand of cDNA, and the addition of 2nd Strand Marking Bu er and 2nd StrandAfter end repair, addition of base A, sequencing connector, magnetic bead screening and recovery of the target fragment, PCR amplification were carried out to complete the entire library preparation work. Enzyme Mix to synthesize the second strand of cDNA.After the library construction is completed, preliminary quantification is performed using Qubit3.0, the library is diluted to 1ng/ul, and then Agilent is used 2000.The raw off machine sequences (Raw Reads) obtained from Illumina platform sequencing are processed through processes such as removing low-quality sequences and connector contamination to obtain high-quality sequences (Clean Reads). All subsequent analyses are based on Clean Reads

value: ovarian cancer

value: shDDP


title: shDDP2


title: snoRNA T183


title: 2C_Ama_36h_11

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. For the parthenogenetic embryos and IVF-derived zygotes, the timing of S-phase was calculated based on the time after activation and insemination, respectively. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment. For the Repli-seq with physically isolated pronuclei, we distinguished maternal and paternal pronucleus based on their size and their relative position to the second polar body and isolated either of them using micromanipulation. The remaining zygote containing a single pronucleus was also collected after removal of polar body so that both pronuclei from the same zygote were further processed for Repli-seq.
Individual blastomeres or pronuclei were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

value: 2-cell embryo + alpha-amanitin

value: (C57BL/6J x CBA) x DBA/2J


title: shDDP1


title: 753_073_Lung - None 0d - old

extract_protocol:
A total of 20 mg of tissue was used for RNA isolation using the Qiazol kit according to manufacturer´s protocol (Qiagen, Hilden, Germany). Quality of RNA was assessed by the Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) using the SS RNA Kit (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries for RNA-seq were prepared using Tru-seq mRNA-Seq Library Prep Kit following manufacturer's protocols.


title: 753_072_Lung - Bleomycin 56d - young

value: Induced Pulmonary Fibrosis

value: young

value: Bleomycin


title: 753_070_Lung - Bleomycin 56d - young

value: Lungs


title: 2C_Ama_36h_10

value: alpha-amanitin


title: sh3

value: sh


title: snoRNA T181


title: sh2


title: 753_069_Lung - Bleomycin 56d - young


title: snoRNA T179


title: 2C_Ama_35h_8


title: 753_068_Lung - Bleomycin 56d - young


title: snoRNA T177


title: 2C_Ama_35h_7


title: 753_067_Lung - NaCl 56d - young

value: Healthy

value: NaCl


title: 2C_Ama_35h_4


title: shNC2

value: shNC


title: snoRNA T175


title: 753_066_Lung - NaCl 56d - young


title: 2C_Ama_35h_5


title: sh1


title: 753_065_Lung - NaCl 56d - young


title: shNC1


title: snoRNA T173


title: snoRNA T171


title: 2C_Ama_35h_3


title: snoRNA T169


title: 2C_Ama_35h_2


title: 2C_Ama_35h_1


title: snoRNA T168


title: MIR193BHG-OE, replicate 2

city: Zhengzhou

first: Ping

last: Wang

address: Kangfu Front Street

institute: The Third Affiliated Hospital of Zhengzhou University

description:
OE_2
gene_expression.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2.
Gene abundance measurements were generationed and normalized  using Stringtie; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM) .
Differential expression were analysed  using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent and extracted with chloroform. 1ug of total RNA was utilized for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: MIR193BHG overexpression


title: MIR193BHG-OE, replicate 3

description:
OE_3
gene_expression.txt


title: 2C_Ama_34h_64


title: shNC3


title: 753_054_Lung - Bleomycin 42d - young


title: MIR193BHG-OE, replicate 1

description:
OE_1
gene_expression.txt


title: 2C_Ama_34h_63


title: snoRNA T167


title: snoRNA T176


title: 753_053_Lung - Bleomycin 42d - young


title: 2C_Ama_34h_62


title: 753_063_Lung - NaCl 56d - young


title: snoRNA T165


title: 753_052_Lung - Bleomycin 42d - young


title: snoRNA T166


title: MIR193BHG-NC, replicate 1

description:
NC_1
gene_expression.txt

value: control


title: 753_051_Lung - Bleomycin 42d - young


title: 753_064_Lung - NaCl 56d - young


title: MIR193BHG-NC, replicate 2

description:
NC_2
gene_expression.txt


title: 2C_Ama_34h_61


title: 2C_Ama_34h_60


title: 753_050_Lung - Bleomycin 42d - young


title: 2C_Ama_34h_59


title: snoRNA T157


title: 2C_Ama_34h_58


title: 753_048_Lung - NaCl 42d - young


title: 2C_Ama_34h_57


title: 753_047_Lung - NaCl 42d - young


title: snoRNA T156


title: snoRNA T155


title: 753_046_Lung - NaCl 42d - young


title: MIR193BHG-NC, replicate 3

description:
NC_3
gene_expression.txt


title: snoRNA T152


title: 2-Cell_40h_48

source_name: 2-cell embryo

value: 2-cell embryo


title: 753_045_Lung - NaCl 42d - young


title: snoRNA T150

value: CD138 enriched tissue


title: snoRNA T161


title: 753_044_Lung - Bleomycin 35d - young


title: 2-Cell_40h_46


title: 2-Cell_40h_44


title: snoRNA T143


title: 753_043_Lung - Bleomycin 35d - young


title: snoRNA T158


title: 753_042_Lung - Bleomycin 35d - young


title: 2-Cell_40h_43


title: 753_040_Lung - NaCl 35d - young


title: snoRNA T136


title: 2-Cell_40h_42


title: 2-Cell_40h_47


title: snoRNA V41FLN


title: 2-Cell_40h_45


title: 753_036_Lung - NaCl 35d - young


title: 2-Cell_39h_40


title: snoRNA UM8ZSV


title: snoRNA T144


title: 2-Cell_39h_38


title: snoRNA T137


title: snoRNA T142


title: 2-Cell_39h_37


title: snoRNA T141


title: 753_049_Lung - NaCl 42d - young


title: 753_034_Lung - Bleomycin 28d - young


title: 753_041_Lung - Bleomycin 35d - young


title: 753_033_Lung - Bleomycin 28d - young


title: snoRNA T140


title: snoRNA XYZ1LW


title: PC9 cells, Control, Hour 24 [PC-9-3]

city: Guangzhou

first: Junwen

last: Ou

address: 3 Hongfu Road, Panyu District

institute: Clifford Hospital, Jinan University

data_processing:
Basecalls performed using  Solexa pipeline v1.8.
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）.
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0).
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: Lung

growth_protocol: H1299 and PC9 cells werecultured in RPMI1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: Cells were seeded into 96-well plates at the density of 5000 cells/well, and were treated or untreated with IC50 concentrations of VitC for 1 h, washed with PBS, and further incubated for 24 h.

value: Lung

value: Lung adenocarcinoma tissue

value: Control, Hour 24


title: PC9 cells, Control, Hour 24 [PC-9-2]


title: snoRNA T138


title: 2-Cell_39h_39

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

institute: Helmholtz Zentrum München

data_processing:
Sequencing reads were aligned to the mm10 genome using bowtie2 (version 2.3.5) with the --local option. Duplicates were marked using samtools (version 1.9)and reads were filtered by keeping only properly paired reads, removing duplicates and selecting those whose mapping quality was higher or equal to 20. Bed files of the read coordinates were generated with bedtools (version 2.29.0) bamtobed command. Using bedtools intersect, read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM and then each bin by its respective average of all samples within the same stage, aiming to correct for the mappability biases intrinsic to the genomic regions. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.28.0) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 1.2.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
Assembly: mm10
Supplementary files format and content: tab-separated txt file with binary replication status
Library strategy: Single-cell Repli-seq

value: (C57BL/6J x CBA) x DBA/2J


title: 2-Cell_40h_41


title: snoRNA T135


title: 753_038_Lung - NaCl 35d - young

city: Biberach

first: Katrin

last: Fundel-Clemens

address: Birkendorfer 65

institute: Boehringer Ingelheim

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using hg38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html).  Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences.   For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25 for human. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Assembly: GRCm38.86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: 753_037_Lung - NaCl 35d - young


title: snoRNA SJJQ37


title: 753_031_Lung - Bleomycin 28d - young

value: Induced Pulmonary Fibrosis


title: 753_030_Lung - NaCl 28d - young

value: young


title: PC9 cells, Vitamin C, Hour 24 [PC-9+VC-3]

value: Vitamin C, Hour 24


title: 753_029_Lung - NaCl 28d - young

value: Lungs


title: 2-Cell_39h_34


title: 753_028_Lung - NaCl 28d - young


title: PC9 cells, Vitamin C, Hour 24 [PC-9+VC-1]


title: 2-Cell_39h_33


title: 2-Cell_38h_32


title: 753_035_Lung - Bleomycin 28d - young

value: Bleomycin


title: 2-Cell_39h_36


title: 2-Cell_38h_31


title: 2-Cell_38h_30


title: 753_027_Lung - NaCl 28d - young


title: 2-Cell_39h_35


title: snoRNA QT1HKR


title: 753_032_Lung - Bleomycin 28d - young


title: PC9 cells, Control, Hour 24 [PC-9-1]


title: NCI-H1299 cells, Control, Hour 24 [1299-3]

value: lymph nodes


title: NCI-H1299 cells, Control, Hour 24 [1299-2]


title: PC9 cells, Vitamin C, Hour 24 [PC-9+VC-2]


title: 2-Cell_38h_28


title: snoRNA QTRAVT


title: 753_026_Lung - NaCl 28d - young

value: Healthy


title: NCI-H1299 cells, Control, Hour 24 [1299-1]


title: 2-Cell_38h_29


title: snoRNA MPT52W


title: snoRNA QGFVJW


title: snoRNA T148


title: 753_025_Lung - Bleomycin 21d - young


title: 753_023_Lung - Bleomycin 21d - young


title: snoRNA KU3SG4


title: 753_024_Lung - Bleomycin 21d - young


title: snoRNA K1JTUA


title: snoRNA MKV237

description:
relapsed or refractory multiple myeloma
total RNA


title: 2-Cell_38h_26


title: 2-Cell_38h_27


title: NCI-H1299 cells, Vitamin C, Hour 24 [1299+VC-3]


title: NCI-H1299 cells, Vitamin C, Hour 24 [1299+VC-1]


title: 753_022_Lung - Bleomycin 21d - young


title: snoRNA F2UFPQ


title: 2-Cell_38h_25


title: 2-Cell_37h_24


title: 753_020_Lung - NaCl 21d - young

value: NaCl


title: snoRNA EP4C6K


title: 2-Cell_37h_23


title: 753_019_Lung - NaCl 21d - young


title: 2-Cell_37h_22


title: 753_018_Lung - NaCl 21d - young


title: snoRNA CSU6UB


title: 2-Cell_37h_20


title: 2-Cell_37h_21


title: 753_016_Lung - NaCl 21d - young


title: 2-Cell_37h_19


title: NCI-H1299 cells, Vitamin C, Hour 24 [1299+VC-2]


title: snoRNA 77PSEW


title: 753_015_Lung - Bleomycin 14d - young


title: Pharmacoresistant epilepsy, Cortex, right frontal lobe, snRNA-seq

city: San Francisco

first: Kun

last: Leng

state: Calfironia

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

data_processing:
Processing and mapping of raw reads from snRNA-seq and cell calling were performed with Cell Ranger (v7.1.0) using GRCh38-2020-A with inclusion of intronic regions as the reference genome.
Assembly: GRCh38-2020-A with inclusion of intronic regions
Supplementary files format and content: HDF5 file of the filtered barcode-feature matrix

molecule: nuclear RNA

source_name: Brain

extract_protocol:
snRNA-seq was performed on fresh frozen brain tissue from the patient’s second epileptic focus resection. 128 mg of frozen brain tissue was cut at –20 °C and sent on dry ice to Singulomics (New York) for nuclei extraction and snRNA-seq using the 10x Genomics v3 platform, targeting recovery of 10,000 nuclei and 25,000 reads per cell.~200 million PE150 reads were sequenced on an Illumina NovaSeq 6000 sequencer.
The library (10x v3.1 GEM) was constructed according to standard operating procedure at Singulomics

value: Brain

value: child

value: Mosaic chromosome 1q gain

value: pharmacoresistant epilepsy


title: U87 cells, DMSO 2

city: Suzhou

first: Gen

last: Li

state: Jiangsu

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

data_processing:
Illumina Casava v 1.8
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: U87 cells were cultured in DMEM with 10% FBS, 1% penicillin and streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Glioblastoma

value: WT

value: DMSO


title: U87 cells, MZ1 2


title: U87 cells, MZ1 1


title: 2-Cell_37h_18

value: 2-cell embryo


title: 753_013_Lung - Bleomycin 14d - young


title: 2-Cell_37h_17

value: (C57BL/6J x CBA) x DBA/2J


title: RNA expression in T-ALL PDX line with 300nM Nav and 1.5uM Ida, biological replicate 2

city: St. Louis

first: Daniel

middle: C

last: Link

address: 660 South Euclid Avenue

department: Medicine/Oncology

institute: Washington University School of Medicine in St. Louis

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8 software.   #All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified. Demultiplexed reads were then used to determine the number of unique occurances of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were written to file along with the barcode's count. All other reads and barcodes were discarded. Gene counts were processed using the R/Bioconductor package EdgeR, with TMM normalization.
Supplementary files format and content: Gene counts per sample

source_name: T-ALL PDX

growth_protocol: PDX cells thawed from cryopreservation and allowed to recover until they were doubling regularly. Cells were grown in StemSpan TMSFEM II (#9655, Stem Cell Technologies), penicillin-streptomycin (100 U/mL), human IL-2 (0.2 IU/mL), human IL-7 (10 ng/mL), and human stem cell factor (50 ng/mL).

extract_protocol:
After culturing for 16 hours cells in drug, RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB). Three replicate samples were treated and isolated.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was blocked using FastSelect reagents (Qiagen 334385) during cDNA synthesis. RNA was fragmented in reverse transcriptase buffer with FastSelect reagent and heating to 94 degrees for 5 minutes, 75 degrees for 2 minutes, 70 degrees for 2 minutes, 65 degrees for 2 minutes, 60 degrees for 2 minutes, 55 degrees for 2 minutes, 37 degrees for 5 minutes, 25 degrees for 5 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: 300nM Navitoclax, 1.5uM Idasanutlin, both Navitoclax and Idasanutlin, or a vehicle control of 0.1% DMSO in media was added to cells.

value: T-ALL PDX

tag: strain

value: 300nM Nav and 1.5uM Ida


title: 2-Cell_35h_9


title: 753_012_Lung - Bleomycin 14d - young

value: Induced Pulmonary Fibrosis

value: young


title: snoRNA 21Z2S9

value: CD138 enriched tissue


title: 753_017_Lung - NaCl 21d - young

value: Lungs


title: U87 cells, DMSO 1


title: RibomethSeq T210

description: newly diagnosed multiple myeloma

data_processing:
Adapter sequences removal, quality and minimum length (15) trimming was applied using Cutadapt.
Reads were mapped using Bowtie2 to a reference sequence file containing rDNA sequences of U18, U28 and U5.8S and splicosomal RNA U1, U12, U2, U4, U5 and U6.
For each position the number of 5’-read ends was counted.
2’O-methyation was calculated as scoreC based on 5’-end frequencies as described before by Birkedal et al., 2015
Assembly: Annotation of modification sites as well as rRNA sequence was downloaded from https://www-snorna.biotoul.fr. Furthermore we considered novel sites reported by Krogh 2016, Jorjani 2016 and Sharma 2017.
Supplementary files format and content: RiboMethSeq_scoreC.txt contains calculated scoreC for annotated modification sites: subunit TAB pos TAB annotation TAB sample_scoreC

extract_protocol:
Multiple myeloma plasma cells were purified using CD138 (Miltenyi Biotech, Bergisch Gladbach, Germany). Total RNA was isolated with the AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. : 80224, Qiagen,  Hilden, Germany) according to the manufacturer’s manual.
100 ng total RNA was fragmented by alkaline hydrolysis at 95°C for 12 min. to achieve a fragment length of about 30 nucleotides. Libraries were prepared using the NEBNext® Small RNA library prep kit.


title: 2-Cell_35h_8


title: RNA expression in T-ALL PDX line with 300nM Nav and 1.5uM Ida, biological replicate 3


title: 753_011_Lung - Bleomycin 14d - young

value: Bleomycin


title: RNA expression in T-ALL PDX line with 300nM Nav and 1.5uM Ida, biological replicate 1


title: RibomethSeq T235

description: newly diagnosed multiple myeloma


title: RibomethSeq T202

description: newly diagnosed multiple myeloma


title: 753_014_Lung - Bleomycin 14d - young


title: RNA expression in T-ALL PDX line with 1.5uM Ida, biological replicate 1

value: 1.5uM Ida


title: RibomethSeq T233

description: newly diagnosed multiple myeloma


title: RibomethSeq T201

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_79


title: 2-Cell_35h_7


title: 753_010_Lung - NaCl 14d - young

value: Healthy

value: NaCl


title: 753_009_Lung - NaCl 14d - young


title: RNA expression in T-ALL PDX line with 1.5uM Ida, biological replicate 2


title: RibomethSeq T230

description: newly diagnosed multiple myeloma


title: RNA expression in T-ALL PDX line with 300nM Nav, biological replicate 3

value: 300nM Nav


title: RibomethSeq T198

description: newly diagnosed multiple myeloma


title: RNA expression in T-ALL PDX line with 300nM Nav, biological replicate 2


title: 753_008_Lung - NaCl 14d - young


title: RibomethSeq T200

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_78


title: RibomethSeq T197

description: newly diagnosed multiple myeloma


title: RNA expression in T-ALL PDX line with 300nM Nav, biological replicate 1


title: 753_006_Lung - NaCl 14d - young


title: 753_007_Lung - NaCl 14d - young


title: 2-Cell_35h_77


title: RNA expression in T-ALL PDX line with DMSO control, biological replicate 3

value: DMSO control


title: RibomethSeq T195

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_76


title: RibomethSeq T183

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_75


title: 753_005_Lung - None 0d - young


title: RNA expression in T-ALL PDX line with DMSO control, biological replicate 1


title: 753_004_Lung - None 0d - young


title: RibomethSeq T181

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_74


title: RibomethSeq T176

description: newly diagnosed multiple myeloma


title: 753_003_Lung - None 0d - young


title: 753_002_Lung - None 0d - young


title: RNA expression in T-ALL PDX line with DMSO control, biological replicate 2


title: MCF10A-Inducible TAZ-4SA  Dox  72rs RNA-Seq-2

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

data_processing:
The RNA-seq paired-end reads were mapped to the human transcriptome using STAR, based on the human genome assembly GRCh38 and GENCODE gene annotation Version 22.
We used RSEM algorithm to estimate the transcript counts (expected count values) for each known gene in GENCODE v22, based on the alignment to the transcriptome.
Assembly: GRCh38
Supplementary files format and content: RSEM output in tabular plain text file

source_name: mammary gland

growth_protocol: DMEM/F12 medium with 5% horse serum (HS) supply with 20 ng/ml EGF; 0.5 µg/ml hydrocor-tisone; 100 ng/ml Cholera toxin; 10 µg/ml Insulin; 100 units/ml penicillin, 100 µg/ml streptomy-cin. Cells were cultured in a humidified atmosphere of 95% air and 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Life Technologies) according to the manufacturer’s protocol.
RNA library were processed for next generation sequencing at Roswell genomic core facility.

treatment_protocol: 0.05 µg/ml doxycycline was used to treat the cells for 24, 48 and 72hrs

value: mammary gland

value: epithelial cells

value: with Dox 72hrs


title: MCF10A-Inducible TAZ-4SA  Dox  72rs RNA-Seq-3


title: RibomethSeq T175

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_6

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

value: 2-cell embryo


title: E105_Veh_03 RNA-seq

first: Tomohiro

last: Nishino

state: California

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: Single-cell sequencing assay for transposase-accessible chromatin from cardiogenic region from E10.5 mouse embryo from Veh treated normal glycemic female

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (5.0.0) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v4 according to specifications in the tutorials (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: normalized gene-cellbarcode expression matrix in csv format

source_name: Embryonic mouse heart at E10.5

growth_protocol: Timed matings were set up between normal glycemic male mice and either Veh-pretreated normal glycemic female mice or STZ-pretreated hyperglycemic female mice. Morning of plug detection was considered embryonic day (E) 0.5 and embryos were harvested at E10.5

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes and resuspended in 35ul of PBS/1% FBS

value: wild type

tag: specific heart region

value: Cardiogenic region

tag: additional cell lineages present in dataset

value: Non-cardiac mesoderm, ectoderm and endoderm

value: vehicle


title: MCF10A-Inducible TAZ-4SA  Dox  72rs RNA-Seq-1

tag: cell line

tag: cell type


title: RibomethSeq T173

description: newly diagnosed multiple myeloma


title: E105_Veh_02 RNA-seq


title: 2-Cell_35h_5

value: (C57BL/6J x CBA) x DBA/2J


title: RibomethSeq T171

description: newly diagnosed multiple myeloma

value: CD138 enriched tissue


title: MCF10A-Inducible TAZ-4SA  Dox  48hrs RNA-Seq-3

value: with Dox 48hrs


title: 2-Cell_35h_4


title: E105_Veh_01 RNA-seq


title: MCF10A-Inducible TAZ-4SA  Dox  48hrs RNA-Seq-2


title: RibomethSeq T169

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_73


title: 2-Cell_35h_3


title: RibomethSeq T167

description: newly diagnosed multiple myeloma


title: MCF10A-Inducible TAZ-4SA  Dox  48hrs RNA-Seq-1


title: MCF10A-Inducible TAZ-4SA  Dox  24hrs RNA-Seq-3

value: with Dox 24hrs


title: MCF10A-Inducible TAZ-4SA  Dox  24hrs RNA-Seq-2


title: 2-Cell_35h_1


title: 2-Cell_35h_2


title: RibomethSeq T161

description: newly diagnosed multiple myeloma


title: RibomethSeq T157

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_16


title: RibomethSeq T144

description: newly diagnosed multiple myeloma


title: MCF10A-Inducible TAZ-4SA  Dox  24hrs RNA-Seq-1


title: 2-Cell_35h_15


title: MCF10A-Inducible TAZ-4SA No Dox RNA-Seq-3

value: without Dox


title: 2-Cell_35h_14


title: IOCircle,Red1,Input,Biol Rep2

city: New York

first: Andreas

last: Hochwagen

state: New York

address: 100 Washington Square East, 1009 Silver Center

institute: New York University

data_processing:
ChIP-seq reads trimmed for low-quality sequence and mapped to a custom hybrid S288C/SK1 genome using bowtie v1.2.0 with parameters -q -m 1 -v 0 -p 8 -S
Peaks called using macs2 v2.1.1 command “callpeak” with parameters --keep-dup="auto" -B --nomodel --extsize 200 --SPMR -g 2.4e7
Normalized signal track produced by comparing ChIP treatment against input control using macs2 v2.1.1 command “bdgcmp” with parameter -m FE
Assembly: Genome_build: Custom hybrid S288C/SK1 genome built by concatenating recently published S288C and SK1 genome assemblies (Yue et al. Nat. Genet. 2017). For syn4 strains, the hybrid genome was built by concatenating genome assemblies of SK1 and S288C with the syn4 chromosome.
Supplementary files format and content: Supplementary_files_format_and_content: bedGraph files: Fold enrichment of ChIP signal track compared to input sample at each base position

organism: Saccharomyces cerevisiae

source_name: Cell suspension in synchronous meiosis

growth_protocol: Synchronous meiosis cultures were prepared by inoculating BYTA medium at OD600 = 0.3 and growing for 16.5 hours at 30°C. Cells were washed twice with water, resuspended in SPO medium at OD600 = 2.0 and incubated at 30°C.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using KAPA Hyper Prep Kit, with 3µM adapters. Input was 10ng and 9 PCR cycles were used to amplify the DNA. Amplified ChIP DNA between 300 and 500 bp was quantified using qPCR as well as an agilent 2200 TapeStation System. Fragments were sequenced on an illumine NextSeq 500 instrument using a 150-bp single-end sequencing protocol.

tag: time

value: meiotic time-point:3 hours

tag: strain code

value: syn IV (inside out circle)/ chr IV (SK1)

tag: chip antibody

value: chip antibody:input


title: IOCircle,Red1,ChIP,Biol Rep2

description: AH11836_sam_reps_Syn4BothTelos_SK1_Yue_PM_SPMR_FE.bdg

value: chip antibody:Anti-Red1 (Lot#16440; kind gift of N. Hollingsworth)


title: IOLinear,Red1,Input,Biol Rep2

value: syn IV (inside out linear)/ chr IV (SK1)


title: ROCircle,Red1,Input,Biol Rep2

value: syn IV (rightside out circle)/ chr IV (SK1)


title: MCF10A-Inducible TAZ-4SA No Dox RNA-Seq-2

value: mammary gland

value: epithelial cells


title: RibomethSeq T143

description: newly diagnosed multiple myeloma


title: ROCircle,Red1,ChIP,Biol Rep2

description: AH11837_sam_reps_Syn4BothTelos_SK1_Yue_PM_SPMR_FE.bdg


title: RibomethSeq T142

description: newly diagnosed multiple myeloma


title: 2-Cell_35h_13

value: 2-cell embryo


title: ROLinear,Red1,Input,Biol Rep2

value: syn IV (rightside out linear) / chr IV (SK1)


title: IOLinear,Red1,ChIP,Biol Rep2

description: AH11838_sam_reps_Syn4BothTelos_SK1_Yue_PM_SPMR_FE.bdg


title: MCF10A-Inducible TAZ-4SA No Dox RNA-Seq-1


title: RibomethSeq MPT52W

description: newly diagnosed multiple myeloma


title: ROLinear,Red1,ChIP,Biol Rep2

description: AH11835_sam_reps_Syn4BothTelos_SK1_Yue_PM_SPMR_FE.bdg


title: 2-Cell_35h_11


title: IOLinear,Red1,Input,Biol Rep1


title: MCF10A-Inducible TAZ-4SA add Dox72hrs TAZ ChIP

data_processing:
The  reads were mapped against the latest reference genome hg38 using BWA.
We then used MACS2 to identify significant peaks for all samples from stimulated and unstimulated cells with FDR cutoff 0.01.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
Cells were cross-linked, lysed, and sonicated to generate DNA fragments. The immunoprecipitation was performed using 5 ug antibody to TAZ (Cell Signaling Technologies) or IgG
ChIPed DNAs were processed for next generation sequencing at Roswell genomic core facility.

value: with Dox 72hrs

value: TAZ (Cell Signaling Technologies)


title: MCF10A-Inducible TAZ-4SA add Dox72hrs IgG

value: IgG


title: RibomethSeq K1JTUA

description: newly diagnosed multiple myeloma

value: CD138 enriched tissue


title: 2-Cell_35h_10

value: (C57BL/6J x CBA) x DBA/2J


title: MCF10A-Inducible TAZ-4SA add Dox 48hrs IgG

value: with Dox 48hrs


title: IOLinear,Red1,ChIP,Biol Rep1


title: MCF7,ERα,E2+TCDD, Biol Rep3

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

description: single

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Human Breast Cancer Cell

growth_protocol: MCF-7 human breast cancer cells (HTB-22, ATCC) were cultured in low-glucose (1 g/L) DMEM (Dulbecco’s modified Eagle’s media) supplemented with 1% (v/v) penicillin/streptomycin (P/S) either 10% (v/v) fetal bovine serum (FBS) or 5% dextran coated charcoal (DCC)-treated FBS.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen)
MicroPlex Library Preparation Kit from Diagenode

treatment_protocol: MCF-7 cells were treated with activated charcoal and subject to various ligands or DMSO for 1 hour and the ChIP sequencing experiment was done in triplicates.

value: Human Breast Cancer Cell

value: ERα (Santa Cruz, #sc-542)


title: MCF7,ERα,E2+TCDD, Biol Rep2

description: single


title: IOCircle,Red1,Input,Biol Rep1

value: meiotic time-point:3 hours

value: syn IV (inside out circle)/ chr IV (SK1)


title: MCF10A-Inducible TAZ-4SA add Dox 48hrs TAZ ChIP


title: 2-Cell_33h_72


title: 2-Cell_33h_70


title: 2-Cell_33h_71


title: IOCircle,Red1,ChIP,Biol Rep1

value: chip antibody:Anti-Red1 (Lot#16440; kind gift of N. Hollingsworth)


title: 2-Cell_35h_12


title: MCF7,AHR,E2+TCDD, Biol Rep3

description: single

value: AHR (Santa Cruz, #sc-133088)


title: MCF10A-Inducible TAZ-4SA add Dox 24hrs IgG

value: with Dox 24hrs


title: 2-Cell_33h_69


title: MCF10A-Inducible TAZ-4SA add Dox 24hrs TAZ ChIP

value: mammary gland


title: MCF7,ERα,E2+TCDD, Biol Rep1

description: single


title: MCF10A-Inducible TAZ-4SA No Dox IgG

value: epithelial cells

value: without Dox


title: MCF7,AHR,E2+TCDD, Biol Rep2

description: single


title: ROCircle,Red1,ChIP,Biol Rep1

value: syn IV (rightside out circle)/ chr IV (SK1)


title: ROCircle,Red1,Input,Biol Rep1

value: chip antibody:input


title: MCF7,AHR,E2+TCDD, Biol Rep1

description: single


title: 2-Cell_33h_68

value: 2-cell embryo


title: MCF10A-Inducible TAZ-4SA No Dox TAZ ChIP

value: TAZ (Cell Signaling Technologies)


title: MCF7,ERα,TCDD, Biol Rep3

description: single


title: 2-Cell_33h_67


title: ROLinear,Red1,Input,Biol Rep1

value: syn IV (rightside out linear) / chr IV (SK1)


title: MCF10A-Inducible TAZ-4SA add Dox ATAC-Seq-2

data_processing:
We first aligned the ATAC-seq paired-end sequencing reads to the human reference genome hg38 using aligner BWA
We then identified accessible regions or “peaks” by MACS2 with cutoff FDR 0.05. Two biological replicates of each condition – No Dox or Dox – were pooled.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
50,000 cells were harvested, and transposition reaction were performed. Following transposition.
DNA was purified using a Qiagen MinElute PCR Puriﬁ-cation Kit and PCR amplified for 10 cycles. Quality of ATAC-seq libraries were qualified with Bioanalyzer and next generation sequencing were performed by Roswell genomic core facility.

treatment_protocol: 0.05 µg/ml doxycycline was used to treat the cells 72hrs

value: with Dox


title: MCF7,ERα,TCDD, Biol Rep2

description: single


title: S288c WT / SK1 WT, Input, Biol Rep 1 b

value: S288c WT / SK1 WT


title: ROLinear,Red1,ChIP,Biol Rep1


title: MCF10A-Inducible TAZ-4SA add Dox ATAC-Seq-1


title: S288c WT / SK1 WT, ChIP, Biol Rep 1 b

description: AH10515_reps_YueSK1_S288C_PM_SPMR_FE.bdg


title: MCF10A-Inducible TAZ-4SA No Dox ATAC-Seq-2


title: MCF7,ERα,TCDD, Biol Rep1

description: single

value: Human Breast Cancer Cell


title: MCF7,AHR,TCDD, Biol Rep3

description: single


title: 2-Cell_33h_65

value: (C57BL/6J x CBA) x DBA/2J


title: MCF10A-Inducible TAZ-4SA No Dox ATAC-Seq-1


title: 2-Cell_33h_64


title: Heterogyzous chrIV(cen4∆)-chrI,Input,Biol Rep 2

value: meiotic time-point:3 hours

value: S288c chrIV-chrI,cen4{delta}/SK1 WT


title: 2-Cell_33h_63


title: HPMVEC_TGF-β1+IL-1β+acetate, rep3

city: St. Petersburg

first: JIANHUA

last: XIONG

state: FL

address: 501 6th Ave South, REB Bldg, 3rd Floor, Rm 3111, REB/Rm 3111

institute: Johns Hopkins University/Johns Hopkins All Children's Hospital

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads. Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping.
Assembly: GRCh38
Supplementary files format and content: The processed data file is in txt format and reports counts

source_name: human pulmonary microvascular endothelial cells (HPMVECs)

growth_protocol: Primary human endothelial cells were cultured using Endothelial Cell Growth Medium MV2 Kit (C-22121; PromoCell).

extract_protocol:
Total RNAs were isolated using RNeasy Plus 96 Kit (74192, Qiagen).
RNA libraries for RNA-seq were constructed according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760L, New England BioLabs).

treatment_protocol: Primary human endothelial cells were treated with or without 10 ng/mL TGF-β1 and 1 ng/mL IL-1β, and with or without 40 mM acetate for 4 days.


title: MCF7,AHR,TCDD, Biol Rep2

description: single


title: Heterogyzous chrIV(cen4∆)-chrI,ChIP,Biol Rep 2

description: AH10514_reps_YueSK1_S288C_PM_SPMR_FE.bdg

value: chip antibody:Anti-Red1 (Lot#16440; kind gift of N. Hollingsworth)


title: 2-Cell_33h_62


title: MCF7,AHR,TCDD, Biol Rep1

description: single

value: AHR (Santa Cruz, #sc-133088)


title: Heterogyzous chrIV–chrI(cen1∆),Input,Biol Rep 2

value: S288c chrIV-chrI,cen1{delta}/SK1 WT


title: MCF7,ERα,RES, Biol Rep3

description: single

value: ERα (Santa Cruz, #sc-542)


title: 2-Cell_33h_66


title: 2-Cell_33h_61


title: HPMVEC_TGF-β1+IL-1β+acetate, rep2

value: human pulmonary microvascular endothelial cells (HPMVECs)


title: Heterogyzous chrIV–chrI(cen1∆),ChIP,Biol Rep 2

description: AH10513_reps_YueSK1_S288C_PM_SPMR_FE.bdg


title: HPMVEC_TGF-β1+IL-1β, rep3


title: Homogyzous chrIV(cen4∆)-chrI,Input,Biol Rep 2


title: HPMVEC_TGF-β1+IL-1β+acetate, rep1


title: 2-Cell_33h_60


title: RibomethSeq T227

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

description: newly diagnosed multiple myeloma

value: CD138 enriched tissue


title: MCF7,ERα,RES, Biol Rep1

description: single


title: 2-Cell_33h_59


title: Homogyzous chrIV(cen4∆)-chrI,ChIP,Biol Rep 2

description: AH10512_reps_YueSK1_S288C_PM_SPMR_FE.bdg


title: HPMVEC_TGF-β1+IL-1β, rep2


title: 2-Cell_33h_58


title: MCF7,AHR,RES, Biol Rep3

description: single


title: HPMVEC_TGF-β1+IL-1β, rep1


title: MCF7,AHR,RES, Biol Rep2

description: single


title: Homogyzous chrIV–chrI(cen1∆),ChIP,Biol Rep 2

description: AH10905_reps_YueSK1_S288C_PM_SPMR_FE.bdg


title: Homogyzous chrIV–chrI(cen1∆),Input,Biol Rep 2


title: MCF7,AHR,RES, Biol Rep1

description: single


title: S288c WT / SK1 WT, Input, Biol Rep 1


title: MCF7,ERα,RES, Biol Rep2

description: single


title: 2-Cell_32h_56


title: HPMVEC_control, rep3

value: Control


title: HPMVEC_control, rep1


title: MCF7,ERα,E2, Biol Rep3

description: single


title: 2-Cell_33h_57


title: MCF7,ERα,E2, Biol Rep2

description: single


title: 2-Cell_32h_55


title: S288c WT / SK1 WT, ChIP, Biol Rep 1


title: HAEC_TGF-β1+IL-1β+acetate, rep3

source_name: human aortic endothelial cells (HAECs)

value: human aortic endothelial cells (HAECs)


title: Heterogyzous chrIV(cen4∆)-chrI,Input,Biol Rep 1

value: chip antibody:input


title: MCF7,ERα,E2, Biol Rep1

description: single


title: 2-Cell_32h_53

value: 2-cell embryo


title: HAEC_TGF-β1+IL-1β+acetate, rep2


title: Heterogyzous chrIV(cen4∆)-chrI,ChIP,Biol Rep 1


title: HPMVEC_control, rep2


title: HAEC_TGF-β1+IL-1β+acetate, rep1


title: 2-Cell_32h_52


title: MCF7,AHR,E2, Biol Rep1

description: single


title: Heterogyzous chrIV–chrI(cen1∆),ChIP,Biol Rep 1


title: HAEC_TGF-β1+IL-1β, rep3


title: 2-Cell_32h_51


title: Heterogyzous chrIV–chrI(cen1∆),Input,Biol Rep 1


title: 2-Cell_32h_50


title: HAEC_TGF-β1+IL-1β, rep2


title: RNA expression in T-ALL PDX line with 1.5uM Ida, biological replicate 3

value: T-ALL PDX

value: 1.5uM Ida


title: MCF7,IgG,DMSO, Biol Rep3

description: single

value: IgG (Santa Cruz, #sc-2027)


title: 2-Cell_32h_54


title: HAEC_TGF-β1+IL-1β, rep1


title: Homogyzous chrIV(cen4∆)-chrI,ChIP,Biol Rep 1


title: Homogyzous chrIV(cen4∆)-chrI,Input,Biol Rep 1


title: 2-Cell_35h_80


title: MCF7,IgG,DMSO, Biol Rep2

description: single

value: Human Breast Cancer Cell


title: HAEC_control, rep3


title: 16-Cell_80h_48

source_name: 16-cell embryo

value: 16-cell embryo

value: (C57BL/6J x CBA) x DBA/2J


title: Homogyzous chrIV–chrI(cen1∆),ChIP,Biol Rep 1

value: meiotic time-point:3 hours


title: 16-Cell_80h_47


title: HAEC_control, rep2


title: MCF7,ERα,DMSO,Biol Rep3

description: single


title: MCF7,AHR,E2, Biol Rep3

description: single


title: MCF7,AHR,E2, Biol Rep2

description: single


title: 16-Cell_80h_46


title: HAEC_control, rep1