title: day 31 - 600 cells 600 um

city: Neuherberg

first: Sandra

last: Wiedenmann

address: Ingolstädter Landstraße 1

department: Helmholtz Pioneer Campus

institute: Helmholtz Zentrum München

data_processing:
For the alignment of reads we used the sequences and annotation files for the human genome (GRCh38) from Ensembl (release 99).
Additionally, we added the sequence of Gfp to the genome. The Cell Ranger software (from 10X Genomics, Pleasanton, CA, version 3.1.0) run with the command ‘cellranger mkref’ created an index of the genome.
The Cell Ranger pipeline run with the command ‘cellranger count’ aligned the reads, generated QC metrics, estimated the number of valid barcodes and created the count matrices.
The command was executed with standard parameters, except that we adjusted the number of expected cells and the chemistry parameter accordingly.
AnnData objects of the raw and filtered count matrices were created using the Python package Scanpy ( version 1.4.4). The alignment files (bam) were sorted by barcode using samtools ( version 1.10) and Velocyto ( version 0.17.17) was run using the ‘velocyto run’ command with the filtered barcodes list from the Cell Ranger run.
Genome_build: hg19
Supplementary_files_format_and_content: compressed matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Wiedenmann_processed_data.csv.gz: concatenated, normalized, logarithmized and batchcorrected counts with clusterannotations for all analyzed cells

source_name: hiPSCs

growth_protocol: HiPSCs were cultured on hESC Matrigel-precoated plates according to manufacturer’s recommendations (Corning) in mTeSR1 medium (Stemcell Technologies) at 5% CO2, 5% O2, and 37°C with daily medium change.

extract_protocol:
While pancreas progenitors at day 13 were harvested with TrypLE Select, organoids on the chip were harvested at day 14, 16, 20, 23, 27 (samples from experiment 2: 600 cells, 300 µm micro-well diameter), and 31 (samples from experiment 1: 300 cells, 300 µm micro-well diameter and 600 cells, 600 µm micro-well diameter) by washing the chip several times with PBS. For the dissociation of pancreatic duct-like organoids into single cells, the organoids were incubated in Accutase (Sigma) for 30-45 min at 37°C. In experiment 2, single cells were cryo-preserved in DMEM with 10% heat-inactivated FBS (Thermo Fisher Scientific) and 10% DMSO based on a previously described scRNA-seq sample preparation protocol56. For sequencing, cryo-preserved cells were thawed in DMEM:F12 and then live-dead filtered like described in the 10x Genomics protocol CG000093. Cells from Experiment 1 (Fig. 2a) were not cryo-preserved and not filtered, but directly processed for actual scRNA-seq measurements.
RNA libraries were prepared for sequencing using standard Illumina and 10xGenomics protocols

treatment_protocol: HiPSCs were differentiated into PPs in a monolayer culture. In brief, 2.5x 10^5 hiPSCs were seeded in mTeSR1 with 10 µM Rock inhibitor per well of a 24-well plate, precoated with growth factor reduced matrigel (1:18 in DMEM:F12, Corning). For the first 6 days, cells were differentiated in the backbone media BE1: MCDB131 (Invitrogen) supplemented with 1% Glutamax (Gibco), 0.8 g/L glucose (Sigma), 1.174 g/L sodium bicarbonate (Sigma), and 5 g/L fatty acid free (FAF) Bovine Serum Albumin (BSA) (Proliant). While 100 ng/mL Activin A (PeproTech) and 2 µM GSK3β-inhibitor (CHIR99021) (Axon MedChem) were added for 24 h, the medium contained 100 ng/mL Activin A and 5 ng/mL bFGF (Novoprotein) for the following two days. From day 3 until day 6 the BE1 media was complemented with 50 ng/mL FGF10 (R&D), 0.75 µM Dorsomorphin (Sigma), and 3 ng/mL mouse Wnt3a (PeproTech). The subsequent backbone media BE3 was composed of MCDB131, 1% Glutamax, 3.3 g/L glucose, 1,754 g/L sodium bicarbonate, 20 g/L FAF-BSA, and 0.5% insulin-transferrin-selenium-X (Gibco). From day 6 until day 9 50 ng/mL FGF10, 200 nM LDN-193189, 0.25 µM SANT-1, 2 µM retinoic acid, and 0.044 g/L L-ascorbic acid (all Sigma) were added. From day 9 until day 13, BE3 media was supplemented with 200 nM LDN-193189, 100 ng/mL EGF (R&D), 10 mM nicotinamide (Sigma), 330 nM Indolactam V (StemCell Technologies), and 0.044 g/L L-ascorbic acid. The media was prepared freshly and changed every day.  For differentiation from pancreas progenitors to pacncreatic duct-like organoids, cells were transferred on the micro-well duct-on-chip platform facilitating a 3D cell culture. For the first seven days on-chip, BE3 medium was supplemented with 1% Penicillin/Streptomycin (Sigma), 10 mM nicotinamide, 10 µM ZnSO4 (Sigma), 50 ng/mL EGF, 50 ng/mL FGF10, 50 ng/mL KGF (PeproTech), 50 nM MSC2530818 (Selleckchem), and 0.044 g/L L-ascorbic acid. 10 µM Rock inhibitor was additionally added for the transfer of PPs on the chip. From day 20 on, cells were differentiated in BE3 containing 1% Penicillin/Streptomycin, 10 mM nicotinamide, 10 µM ZnSO4, 50 ng/mL EGF, 50 n/mL FGF10, and 0.044 g/L L-ascorbic acid. The media was changed twice a week.

tag: experiment

tag: days of differentiation

tag: well diameter in um

tag: cell number per well

tag: culture method

value: 3D cell culture on-chip


title: KO_MPP_H2B-GFP_LOW_RNA_rep_3

status: Public on Jul 08 2021

type: SRA

city: Houston

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 genome assembly using STAR aligner.
Differentially expressed genes were identified using DeSeq2.
Promoter motif analysis was done using HOMER.
Genome_build: mm10

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Mice were housed in AAALAC-accredited, specific-pathogen-free animal care facilities at Baylor College of Medicine (BCM) with 12-hour light-dark cycle and received standard chow ad libitum. All procedures were approved by the BCM (protocol #AN-5858) Institutional Animal Care and Use Committees.

extract_protocol:
HSCs and MPPs were sorted into Trizol and RNA purified according to the manufacturer's instructions. DNase I-treated RNA samples were purified using the QIAGEN MinElute kit before cDNA was made and amplified with a SMART-Seq2 kit.
The cDNA was then fragmented and barcoded for sequencing using a Nextera XT kit.

treatment_protocol: Conditional deletion of Hira in the hematopoietic system was induced by treating mice with 2 doses of 20𝝁g of polyinosinic:polycytidylic acid (poly(I:C)) by intraperitoneal injection skipping one day between each dose. Mice were sacrificed 1 week after the first dose of poly (I:C) and 2500 HSCs and MPPs were sorted into Trizol. To sort HSCs and MPPs based on cell division history following Hira deletion, we used a pulse of H2B-GFP expression  induced in Mx1-Cre; Hirafl/fl; Rosa26-M2rtTA; TetOP-H2B-GFP mice with Doxycycline dissolved in drinking water at 2 mg/ml with 10 mg/ml sucrose to counteract the bitter flavor of Doxycycline and encourage consumption. Doxycycline-treated water was changed every 7-10 days. After a 6-week pulse period, doxycycline treatment was stopped and 2 doses of Poly I:C were administered intraperitoneally with 20 μg every other day for 2 days to induce Hira deletion. These mice were sacrificed after 15 days after the last Poly I:C injection and 17 days after stopping doxycycline treatment (17 day chase period). HSCs and MPPs were then sorted based on their H2B-GFP expression levels.

tag: strain

tag: genotype

value: HIRA KO

tag: cell type

value: Bone marrow multipotent progenitors

tag: h2b-gfp expression

value: H2B-GFP Low


title: Primary breast tissue #4 Sample 4 Cy3

type: RNA

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

description:
Primary breast tissue #4
pre and post treatment tissue from luminal breast cancer patient

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential by SKCCC microarry core facility

scan_protocol: Agilent Technologies Scanner G2505C US22502585 Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: R language and limma package was used for within (Loess) and between array (Aquantile) normalization. Intensity of single color channel was obtained afterwards.

molecule: total RNA

organism: Homo sapiens

label_protocol: 400ng RNA was used for labeling by SKCCC microarry core facility

extract_protocol: Total RNA extracted using Trizol and Qiagen RNeasy purification kit following manufacturer's instructions

tag: tissue

value: breast


title: R2 tumor peripheral tissue

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: tumor core

data_processing:
The raw sequence reads were analyzed by Cell Ranger v.3.0.1 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with read counts for each sample

source_name: Brain

extract_protocol:
CD31+ selection for endothelial cell enrichment was performed using Dynabeads (11155D, Invitrogen).
scRNAseq libraries were prepared using Chromium Single Cell 30 V2/3 Reagent Kit (10X Genomics) according to the manufacturer’s protocol.

value: Brain

tag: age

value: adult


title: Individual #07, EtOH

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: HL2JCBGX9_ccSet46_18s006343-1-1_Malinen_lane1SET4LIB9

data_processing:
Quality control using "afterQC"
Read alignment using "kallisto"
Differential gene expression using "DESeq2"
Genome_build: hg38
Supplementary_files_format_and_content: relative abundance and statistical metrics in Excel table

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 24 h with either 10 nM 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

value: peripheral blood mononuclear cells

tag: treatment

value: 0.1% ethanol for 24 h


title: KO_MPP_H2B-GFP_LOW_RNA_rep_2


title: day 31 - 300 cells 300 um

state: Bavaria

country: Germany


title: Primary breast tissue #3 Sample 3 Cy5

description:
Primary breast tissue #3
pre and post treatment tissue from luminal breast cancer patient


title: Individual #04, EtOH

description: HL2JCBGX9_ccSet46_18s006343-1-1_Malinen_lane1SET4LIB1


title: day 27


title: Individual #06, EtOH

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET7LIB1


title: day 23


title: WT_MPP_H2B-GFP_LOW_RNA_rep_2

value: WT


title: day 20


title: KO_MPP_H2B-GFP_LOW_RNA_rep_1


title: WT_MPP_H2B-GFP_LOW_RNA_rep_1


title: WT_MPP_H2B-GFP_LOW_RNA_rep_3


title: Individual #03, EtOH

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET8LIB1


title: Primary breast tissue #5 Sample 5 Cy3

description:
Primary breast tissue #5
pre and post treatment tissue from luminal breast cancer patient


title: Individual #05, EtOH

description: HL2JCBGX9_ccSet46_18s006343-1-1_Malinen_lane1SET4LIB5


title: day 16


title: cultured_oocyte3_class_IV_20_percent_O2_MAOplusLiCl_PBAT

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Illumina HiSeq 1000; Illumina GAIIx
RRBS reads were trimmed to remove poor quality calls and adapters using Trim Galore v0.3.5 (parameters --rrbs) and mapped to the mouse genome GRCm38 assembly by Bismark (Krueger and Andrews, 2011) v0.14.0. Published bisulfite-sequencing data were processed as described previously (Veselovska et al.). Raw RNA-seq reads were trimmed to remove both poor quality calls and adapters using TrimGalore v.0.2.8 and mapped to GRCm38 using TopHat v.2.0.9 (option –g 1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited file with one line per gene, and RPKM values for each sample
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

molecule: genomic DNA

source_name: cultured oocytes

growth_protocol: The ovaries, aged of seven days old, from C57 Black6 mice were collected and digested with trypsin (Sigma) and collagenase I (Sigma) at 37°C for 15 minutes. The trypsin-collagenase action was stopped with foetal bovine serum (Sigma) and centrifuged for five minutes at 1 600 rpm. The pellet was suspended into warm medium and plated onto a gelatine coated plate. The oocyte culture was performed under two different conditions: 20% O2 and 5%O2. The culture medium was changed every 24 hours for the 5% O2, and every 48 hours for the 20% O2 condition. To reach the appropriate growth size, the oocytes were grown for 9 days under 5% O2 and for 14 days under 20% O2.

extract_protocol:
RRBS Extracted DNA was spiked with a small amount of lambda DNA (0.05pg per 6ng of genomic DNA) for bisulphite conversion control, digested with MspI endonuclease (Fermentas), end-repaired (Klenow fragment exo-, Fermentas, with 10nM dATP, 1nM dCTP and 1nM dGTP) and ligated with 5mC-adaptors (Illumina) with T4 ligase (Fermentas). Bisulphite conversion was done using the EZ DNA Methylation-Direct Kit (Zymo Research) and DNA was amplified by 15 cycles of PCR using Pfu Turbo Cx polymerase (Stratagene). DNA was purified using SPRI beads (Agencourt).  RNA was extracted using TRIsure reagent (Bioline) followed by RNA Clean & Concentrator (Zymo Research) with on-column DNAse treatment (RNasefree DNase I, Life Technologies).
For RNA-seq libraries: Reverse transcription was performed using SuperScript III (Life Technologies), followed by second DNA strand synthesis using dUTPs instead of dTTPs and DNA polymerase I (NEB); libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB), including dUTP excision step by USER Enzyme (NEB) before PCR. RRBS: Extracted DNA was spiked with a small amount of lambda DNA (0.05pg per 6ng of genomic DNA) for bisulphite conversion control, digested with MspI endonuclease (Fermentas), end-repaired (Klenow fragment exo-, Fermentas, with 10nM dATP, 1nM dCTP and 1nM dGTP) and ligated with 5mC-adaptors (Illumina) with T4 ligase (Fermentas). Bisulphite conversion was done using the EZ DNA Methylation-Direct Kit (Zymo Research) and DNA was amplified by 18 cycles of PCR using Pfu Turbo Cx polymerase (Stratagene). DNA was purified using SPRI beads (Agencourt). For PBAT: As in Stewart et al. (2015): Cells were lysed in EB buffer (Qiagen) with 0.5% SDS (Sigma, 161-0418) and bisulfite-treated using theone-stepmodification procedure in the Imprint DNA modification kit(Sigma,MOD50-1KT).The resulting DNA was purified using the EZ DNA methylation direct kit (Zymo, D5020). First strand synthesis was performed using Klenow Exo− (New England Biolabs, M0212S) and a custom streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs (bp) of random sequence (9N). This was followed by exonuclease I treatment (New England Biolabs, M0293S), purification using SPRI beads (1.8× ratio; Fisher Scientific, 09-981123), and binding to biotin beads (Life Technologies, 11205D). Samples were then subjected to second strand synthesis, again using custom primer, followed by 10 cycles of library amplification using Phusion polymerase (Thermo Scientific, F-530S) before final purification using SPRI beads.

treatment_protocol: The oocyte culture was performed under two different conditions: 20% O2 and 5%O2. Each condition has replicate. Also, the oocyte culture model was treated with 100 µM tranycylpromine (Sigma), a MAO inhibitor of KDM1 enzyme and with 15 mM/ml LiCl (Sigma) under 20% O2 condition in triplicate.

value: C57BL/6 Barb

value: oocytes

tag: size

value: 20% oxygen treated MAO+LiCl


title: Individual #02, EtOH

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET7LIB5


title: KO_HSC_H2B-GFP_LOW_RNA_rep_3

value: Bone marrow hematopoietic stem cells


title: Primary breast tissue #2 Sample 2 Cy5

description:
Primary breast tissue #2
pre and post treatment tissue from luminal breast cancer patient


title: cultured_oocyte3_class_IV_20_percent_O2_MAO_PBAT

value: 20% oxygen treated MAO


title: KO_HSC_H2B-GFP_LOW_RNA_rep_2


title: day 14


title: Individual #01, EtOH

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET7LIB9


title: Primary breast tissue #1 Sample 1 Cy3

description:
Primary breast tissue #1
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #3 Sample 3 Cy3


title: KO_HSC_H2B-GFP_LOW_RNA_rep_1


title: cultured_oocyte3_class_IV_20_percent_O2_LiCl_PBAT

value: 20% oxygen treated LiCl


title: Individual #12, 125D

description: H5F7YBGX9_CC-SET1_3_18s005575-1-1_Nurminen_lane1SET3LIB10


title: Primary breast tissue #2 Sample 2 Cy3


title: Primary breast tissue #1 Sample 1 Cy5


title: Healthy_donor-iMCACs_fluid_shear_stress(+)_3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequenced reads from fasq files were mapped to GRCh37/hg19 whole genome using STAR 2.6.0c aligner.
Fragments Per Kilobase of exon per Million mapped reads (FPKM) value of each gene was calculated using GeneData Profiler Genome（version 13.0.11) .
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample .

source_name: 201B7 human iPS cells

growth_protocol: Healthy donor-iMCACs were maintained under 5% CO2 at 37°C in PneumaCult-ALI Basal Medium supplemented with 4 μg/ml Heparin, 1.0 μM Hydrocortisone, 10 µM DAPT and 10 μM Y-27632.

extract_protocol:
Total RNA was extracted using the PureLinkTM RNA mini kit (invitrogen) according to the manufacturer's protocol.
Library preparation was performed with the SMART-Seq v4 Ultra Low Input RNA Kit (TAKARA) and Nextera XT DNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: In "Healthy donor-iMCACs fluid shear stress(+)", the attached cells were perfused with culture medium using a micro peristaltic pump until Day 42. In "Healthy donor-iMCACs cell culture insert" and "Healthy donor-iMCACs fluid shear stress(-)", the cells were not perfused with culture medium. The medium was changed every other day until Day 42.

value: 201B7 human iPS cells

tag: culture condition


title: day 13

value: 2D cell culture


title: WT_HSC_H2B-GFP_LOW_RNA_rep_3


title: Individual #11, 125D

description: H5F7YBGX9_CC-SET1_3_18s005575-1-1_Nurminen_lane1SET3LIB6


title: Individual #10, 125D

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET8LIB10


title: Healthy_donor-iMCACs_fluid_shear_stress(+)_1


title: cultured_oocyte3_class_IV_20_percent_O2_CON_PBAT

value: 20% oxygen treated CON


title: cultured_oocyte2_class_IV_20_percent_O2_MAOplusLiCl_PBAT


title: WT_HSC_H2B-GFP_LOW_RNA_rep_1


title: WT_HSC_H2B-GFP_LOW_RNA_rep_2


title: Healthy_donor-iMCACs_fluid_shear_stress(-)_3


title: Individual #09, 125D

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET8LIB6


title: cultured_oocyte2_class_IV_20_percent_O2_MAO_PBAT


title: cultured_oocyte2_class_IV_20_percent_O2_LiCl_PBAT


title: KO_MPP_H2B-GFP_HIGH_RNA_rep_3

value: HIRA KO

value: Bone marrow multipotent progenitors

value: H2B-GFP High


title: Healthy_donor-iMCACs_fluid_shear_stress(-)_2


title: KO_MPP_H2B-GFP_HIGH_RNA_rep_2


title: Individual #08, 125D

description: H5F7YBGX9_CC-SET1_3_18s005575-1-1_Nurminen_lane1SET3LIB2


title: Healthy_donor-iMCACs_fluid_shear_stress(-)_1


title: Healthy_donor-iMCACs_cell_culture_insert_3


title: Healthy_donor-iMCACs_fluid_shear_stress(+)_2


title: Individual #07, 125D

description: HL2JCBGX9_ccSet46_18s006343-1-1_Malinen_lane1SET4LIB10


title: KO_MPP_H2B-GFP_HIGH_RNA_rep_1


title: Individual #06, 125D

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET7LIB2


title: cultured_oocyte1_class_IV_20_percent_O2_MAOplusLiCl_PBAT


title: cultured_oocyte2_class_IV_20_percent_O2_CON_PBAT


title: Healthy_donor-iMCACs_cell_culture_insert_2


title: Individual #04, 125D

description: HL2JCBGX9_ccSet46_18s006343-1-1_Malinen_lane1SET4LIB2


title: WT_MPP_H2B-GFP_HIGH_RNA_rep_3


title: WT_MPP_H2B-GFP_HIGH_RNA_rep_1


title: Healthy_donor-iMCACs_cell_culture_insert_1


title: cultured_oocyte1_class_IV_20_percent_O2_MAO_PBAT


title: cultured_oocyte1_class_IV_20_percent_O2_LiCl_PBAT


title: cultured_oocyte1_class_IV_20_percent_O2_CON_PBAT

value: 20% oxygen control


title: WT_MPP_H2B-GFP_HIGH_RNA_rep_2


title: KO_HSC_H2B-GFP_HIGH_RNA_rep_3


title: RUNX1-JAK2_cloneF2_dTAG

city: Vienna

first: Klaus

middle: Josef

last: Fortschegger

state: Austria

address: Zimmermannplatz 10

department: Genetics of Leukemia

country: Austria

institute: St. Anna Kinderkrebsforschung

data_processing:
demultiplexed bam files were obtained from the squencing facility
bam to fastq conversion, picard toolsSamToFastq, version 2.7.1-SNAPSHOT
reads were mapped to human genome GRCh38 without alt loci using  STAR 2.7.0b
Count statistics for Refseq genes were obtained by the “featureCounts” function (package Rsubread_1.28.1) using Ensembl annotation Homo_sapiens.GRCh38.100
Gene expression was normalized, batch-corrected and analyzed using DESeq2 version 1.18.1; design "~batch + combined"; including independent filtering with alpha=0.05, cooksCutoff=FALSE; shrunken log2 fold changes using the adaptive shrinkage estimator were calculated
Genome_build: GRCh38 without alt loci ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.g2z
Supplementary_files_format_and_content: raw_counts.txt: Matrix table with raw read counts for every gene and every samples
Supplementary_files_format_and_content: normalized_counts.txt: table including normalized counts for transcripts with gene symbol only; further filtered according to independent filtering alpha=0.05
Supplementary_files_format_and_content: LFC_padj.txt: table including shrunken Log2FC + padj

source_name: hematopoietic cells

growth_protocol: hiPSCs were grown on Matrigel in mTeSR1 medium and differentiated for 12 days with StemDIFF hematopoietic kit

extract_protocol:
TRIzol reagent with glycogen as co-precipitant
polyA-enrichment + stranded NEBNext Ultra II kit

treatment_protocol: differentiating cells were treated for the first day with 3µM CHIR99021 and 11 days either with 100nM dTAG-13 or DMSO vehicle

value: hiPSC-derived hematopoietic cells

tag: condition

value: dTAG

tag: identifier

tag: batch

tag: factor combined


title: cultured_oocyte2_class_IV_5_percent_O2_RRBS

value: 5% oxygen


title: Individual #03, 125D

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET8LIB2

value: peripheral blood mononuclear cells


title: RUNX1-JAK2_cloneF2_DMSO

value: DMSO


title: Individual #02, 125D

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET7LIB6


title: Individual #01, 125D

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET7LIB10


title: KO_HSC_H2B-GFP_HIGH_RNA_rep_2


title: Individual #05, 125D

description: HL2JCBGX9_ccSet46_18s006343-1-1_Malinen_lane1SET4LIB6


title: cultured_oocyte2_class_IV_20_percent_O2_RRBS

value: C57BL/6 Barb

value: oocytes

value: 20% oxygen


title: KO_HSC_H2B-GFP_HIGH_RNA_rep_1

value: Bone marrow hematopoietic stem cells


title: wild-type_3_dTAG

value: parental


title: RUNX1-JAK2_cloneH1_dTAG


title: RUNX1-JAK2_cloneH1_DMSO


title: scH&G AluI

city: Santa Barbara

first: Siddharth

last: Dey

state: CA

address: 3357 Engrg II UCSB

department: Chemical Engineering

institute: UCSB

data_processing:
Library strategy: scH&G
For plates (P1-9) and libraries (L1-3), Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 build using the Burrows-Wheeler Aligner (BWA), filtered for unique mapping full-length reads and demultiplexed. 5hmCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
For scH&G, Fastq files are parsed for library barcodes. Read 1 was trimmed to  76 basepairs and mapped to the hg19 build using the Burrows-Wheeler Aligner (BWA), filtered for unique mapping full-length reads and demultiplexed. BseRI or AluI positions are obtained from the sequencing data using custom scripts in Perl identifying their respective recognition sequence in the hg19 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Text files with 4 columns: Single Cell ID, chromosome, coordinate and strand

source_name: Embryonic stem cell

extract_protocol:
H9 cells were grown on Matrigel (Fisher cat #08-774-552) in mTeSR1 (Stem Cell Technologies cat #85850). Cells were passed in clumps using Versene solution (Thermo fisher scientific cat # 15040066). For sorting, cells were dissociated into single cells using TrypLE, resuspended in 1x PBS, and passed through a cell strainer.
384-well plates containing 4 μL of Vapor-Lock (Qiagen) and 200 nL of lysis buffer (0.0875% IGEPAL CA-630) are prepared and single cells are FACS sorted into each reaction well. After sorting, plates are stored at -80°C until use. The cells were lysed at 65°C for 3 minutes, and reaction wells receive 500 nL of either 1.4x Buffer4 (NEB) [negative control, scAba-Seq only], BseRI mix [1.4x Buffer 4, 0.25 units BseRI (NEB)], AluI mix [1.4x Buffer 4, 0.25 units AluI (NEB)], or a combined mixture containing both BseRI and AluI (1.4x Buffer 4, 0.125 units BseRI, 0.125 units AluI). The plate is incubated for 1 hour at 37°C followed by heat inactivation at 80°C for 20 minutes. Next, 1.8 μL of protease mix (1x Buffer 4, 6 μg Qiagen protease) is added, and the plate is heated to 50°C for 16 hours, 75°C for 20 minutes, and 80°C for 5 minutes. Then 5hmC sites in the genome are glucosylated by adding 500 nL of glucosylation mix [1x Buffer 4, 1x UDP-Glucose (NEB), 1 unit T4-BGT (NEB)] and incubated at 37°C for 16 hours. Afterwards, 500 nL of protease mix (1x Buffer 4, 2 μg Qiagen protease) is added, and the plate is heated to 50°C for 3 hours, 75°C for 20 minutes, and 80°C for 5 minutes. To detect 5hmC, 500 nL of AbaSI reaction mix (1x Buffer 4, 1 unit AbaSI) is added and the plate is incubated at 25°C for 1.5 hours, and 65°C for 25 minutes. Cells receiving the AluI mix or the combined BseRI and AluI mix have 200 μL of 64 nM blunt end adapter added. All cell also receive 200 μL of 75 nM scAba-seq adapters. Ligation mix [1x T4 DNA Ligase reaction buffer (NEB), 4 mM ATP (NEB), 140 units T4 DNA Ligase (NEB)] is then added to bring the total volume of each reaction well to 5 μL. Subsequently, the plate is incubated at 16°C for 16 hours. Excluding the Vapor-Lock, all reagents are dispensed using the Nanodrop II liquid handling robot. After ligation, the reaction wells are pooled.

value: Embryonic stem cell

tag: molecule subtype

value: 5hmC and genomic DNA


title: cultured_oocyte2_class_II_20_percent_O2_RRBS


title: scH&G_BseRI and AluI


title: RUNX1-JAK2_cloneG10_dTAG


title: cultured_oocyte1_class_I_5_percent_O2_RRBS


title: Aba-seq


title: RUNX1-JAK2_cloneG10_DMSO


title: GATA1s T21-FL - GATA1

city: Toronto

first: Elvin

last: Wagenblast

state: ON

address: 101 College Street

department: Princess Margaret Cancer Centre

country: Canada

institute: UHN

data_processing:
Library strategy: CUT&RUN
Fastq files were trimmed using fastp and aligned to the hg38 human genome and to the yeast genome for spike-in quantification using bowtie2.  Peaks were called using MACS2 peak caller.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are in bed format and include called peaks.

source_name: CD34+ cells

growth_protocol: CD34+ cells from N-FL and T21-FL were sorted by flow cytometry and subsequently 2x10^5 cells were CRISPR/Cas9-edited per condition. Edited cells were expanded for 5 days in X-VIVO 10 media.

extract_protocol:
Cells were washed in cold PBS (Thermo Fisher) and spun down at 350xg for 10min at 4°C.
After washing, activated Concanavalin A beads were added. Wash buffer was removed by placing the samples on a magnet and antibody buffer containing 0.0125% of digitonin and GATA1 antibody (Abcam, 1:100) or rabbit gG control antibody (Thermo Fisher, 1:300) was added to the beads. Samples were incubated on a rotator for 2h at 4°C, followed by the addition and activation of pA-MN and isolation of soluble DNA as previously described (Skene et al., 2018). DNA was extracted with the MinElute PCR Purification kit (Qiagen). DNA libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB). Subsequently, libraries were size selected for 150-400bp range with the Pippen HT and size verified with the Bioanalyzer.

treatment_protocol: CRISPR/Cas9 RNP electroporations were carried out using chemically synthesized gRNAs (IDT), recombinant Cas9 nuclease (IDT) and the 4D-Nucleofector (Lonza) as previously described (Wagenblast et al., 2019).

value: Fetal-liver derived hematopoietic stem and progenitor cells

tag: karyotype

value: trisomic fetal liver

value: GATA1s editing

tag: cut&run antibody

value: Rabbit polyclonal anti-GATA1, Abcam, ab11852


title: cultured_oocyte2_class_IV_5_percent_O2_RNAseq


title: cultured_oocyte2_class_IV_20_percent_O2_RNAseq


title: WT_HSC_INPUT

data_processing:
ChIP-seq reads were aligned using Bowtie2.
Data were filtered using deepTools.
Peaks were called using MACS2 and Homer.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

extract_protocol:
HSCs were sorted into PBS + 0.1 mg/ml BSA in DNA LoBind tubes and centrifuged at 2000 rpm for 5 minutes in a swing bucket rotor directly followed by centrifugation in a table-top centrifuge at 7000 rpm for 1 minute. The supernatant was discarded before adding 100 μl TM2 buffer (10 mM Tris [pH 7.4], 2 mM MgCl2, 1 mM CaCl2, 0.6% NP-40) + 1:100 protease inhibitor (Calbiotech) to lyse cells and pipet gently to mix. Samples were incubated on ice for 4 minutes before adding micrococcal nuclease (MNase) depending on the cell number (25 GU for 5K-10K cells = 5 μl of 1:400 MNase diluted in TM2 buffer). Samples were then incubated at 37oC for 2 minutes before adding 100 μl 2xRIPA (20 mM Tris [pH 7.5], 280 mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium deoxycholate, 5 mM EDTA) + 1:100 protease inhibitor (Calbiotech) + 5 μl 0.5M EDTA and centrifuging at 13,200 rpm 15 minutes. Samples were transferred to a 200 μl PCR tube and 20 μl (10%) were taken for input before adding 1 μl antibodies to the remaining 180 μl of sample for IP (anti-H3.3 [MABE872, rat mAb]). Tubes were then rotated at 4oC overnight (12-16 hours). 10 μl of protein-G Dynabeads were washed with 500 μl of 1X RIPA twice in a 1 ml tube and reconstituted by adding 10 μl of 1X RIPA per IP sample. The IP samples were centrifuged briefly to remove liquid on the lid before adding 10 μl of washed Dynabeads to each IP sample. IP samples were then rotated at 4 oC for 2 hours before being centrifuged briefly to remove liquid from caps. Tubes were then placed on a magnetic rack to collect beads before removing and keeping the supernatant to use for an MNase digestion check. Beads were then resuspended in 200 μl 1X RIPA before the beads were again collected on a magnet and the supernatant discarded. This RIPA wash was repeated for a total of 2 RIPA washes. Two LiCl buffer washes were performed in the same way. The beads were then resuspended in 200 μl TE buffer and transferred to a new PCR tube (tube switch). The tubes were placed on a magnet to collect the beads before the TE buffer was discarded. 40 μl TE buffer + 2 μl Proteinase K (10 mg/ml) were then added to IP samples. 20 μl TE buffer + 2 μl Proteinase K (10 mg/ml) were added to input samples. Tubes were incubated at 37 oC for 1 hour. The IP (immunoprecipitated), input, and supernatant DNA was then purified with the ZYMO DNA clean and concentrator kit (1:5 binding buffer). The IP and input DNA were eluted in 40 μl TE buffer. The supernatant DNA was eluted in 10 μl TE buffer and the MNase digestion efficiency was checked on a 5% PAGE gel. A 2.0x SPRI cleanup was then performed and the beads were briefly air dried before resuspension in 5 μl of elution buffer and mixing (did not elute—kept beads through the adaptor ligation reaction).
The NEBNext Ultra II kit was used to generate libraries for Illumina sequencing using adaptors diluted to 1:10 for input samples and 1:25 for IP samples. A 1.3x SPRI cleanup was performed after adaptor ligation and DNA was eluted in 17 μl of elution buffer but only 15 μl were recovered. The cycle number for PCR amplification was then determined by RT-qPCR using 5 μl NEBNext Ultra II Q5 master mix with 0.5 μl 20X SYBR/ROX, 0.5 μl 1:10 diluted barcoded primers (NEB, E7600), 1 μl of IP or input adaptor-ligated DNA, and 3 μl nuclease-free water. The libraries were then amplified with 2 μl of barcoded primers diluted 1:10 (NEB, E7600), 20 μl NEBNext Ultra II Q5 PCR mix, 4.5 μl of IP or input adaptor-ligated DNA, and 13.5 μl nuclease-free water using the cycle number identified for each sample from the CT values found by qPCR. A 1.6x SPRI cleanup was performed followed by a tube switch. An additional 1.6x SPRI cleanup was then performed before beads were air dried and DNA was eluted in 11 μl of elution buffer. 10 μl of each sample were recovered and the KAPA Library Quantification kit was used to determine final library concentrations. 1 μl of final libraries were run on a 5% PAGE gel in 10 μl 1X loading dye to assess library fragment size distributions. Libraries were pooled at 10 nM final concentration and sequenced on an Illumina sequencer.

treatment_protocol: Conditional deletion of Hira in the hematopoietic system was induced by treating mice with 2 doses of 20 ug of polyinosinic:polycytidylic acid (poly(I:C)) by intraperitoneal injection skipping one day between each dose. Mice were sacrificed 1 week after the first dose of poly (I:C) and HSCs were sorted.

value: WT


title: KO_HSC_INPUT

value: HIRA KO


title: cultured_oocyte1_class_IV_5_percent_O2_RRBS


title: GATA1s N-FL - GATA1

value: disomic fetal liver


title: wild-type_2_dTAG

value: hiPSC-derived hematopoietic cells

value: dTAG


title: cultured_oocyte1_class_IV_5_percent_O2_RNAseq

value: 5% oxygen


title: WT_HSC_H2B-GFP_HIGH_RNA_rep_3

value: H2B-GFP High


title: Control N-FL - GATA1

value: Control


title: cultured_oocyte1_class_IV_20_percent_O2_RNAseq

value: C57BL/6 Barb

value: oocytes

value: 20% oxygen


title: wild-type_2_DMSO

value: parental

value: DMSO


title: KO_HSC_H3.3_rep_2

description: ChIP DNA

value: Bone marrow hematopoietic stem cells


title: WT_HSC_H2B-GFP_HIGH_RNA_rep_2


title: KO_HSC_H3.3_rep_1

description: ChIP DNA


title: cultured_oocyte2_class_I_5_percent_O2_RRBS


title: wild-type_3_DMSO


title: RUNX1-JAK2_cloneE5_dTAG


title: scH&G BseRI

value: Embryonic stem cell

value: 5hmC and genomic DNA


title: Stable PDX Nevus donor (human) 3

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

description:
Read counts estimated by using RSEM
stableP_3

data_processing:
The FASTQ files were analyzed by using FastQ Screen-0.14.0. Any sequences specifically matched to mouse genome from PDX samples were removed using FastQ Screen with --filter 03 –inverse options.
The trimmed sequences were aligned to human genome/GRCh38 and transcriptome/ensGene98 by using STAR-2.7.0e.
Sequences located at transcripts were quantified by using RSEM-1.3.1.
Differentially expressed genes (DEG) analysis was performed using DESeq2-1.24.0.
Genome_build: Human genome/GRCh38
Supplementary_files_format_and_content: Read counts estimated by using RSEM

source_name: Skin

growth_protocol: RNA extracted from Human/Mouse Tissue

extract_protocol:
Lysis buffer
Modified SMART-Seq2 cDNA and Illumina NexteraXT library construction. Protocol based on preparation of Single-Cell RNA-Seq libraries for next generation sequencing -Trombetta et al 2017

tag: harvest stage

value: Stable (>100 days)

tag: strain/genotpe

value: Human skin


title: RUNX1-JAK2_cloneE5_DMSO

tag: genotype


title: Stable PDX Nevus donor (human) 2

description:
Read counts estimated by using RSEM
stableP_2


title: Stable PDX Nevus donor (human) 1

description:
Read counts estimated by using RSEM
stableP_1


title: RUNX1-JAK2_cloneC6_dTAG

tag: cell type


title: Reject PDX Nevus donor (human) 3

description:
Read counts estimated by using RSEM
rejectP_3

value: Post-Rejection


title: RUNX1-JAK2_cloneC6_DMSO


title: RUNX1-JAK2_cloneA6_dTAG


title: WT_HSC_H2B-GFP_HIGH_RNA_rep_1

tag: strain

value: WT

tag: h2b-gfp expression


title: WT_HSC_H3.3_rep_2

description: ChIP DNA


title: Control T21-FL - GATA1

value: Fetal-liver derived hematopoietic stem and progenitor cells

value: trisomic fetal liver

value: Rabbit polyclonal anti-GATA1, Abcam, ab11852


title: RUNX1-JAK2_cloneA6_DMSO

value: hiPSC-derived hematopoietic cells


title: WT_HSC_H3.3_rep_1

description: ChIP DNA


title: wild-type_1_dTAG

value: dTAG


title: Reject PDX Nevus donor (human) 2

description:
Read counts estimated by using RSEM
rejectP_2


title: Reject PDX Nevus donor (human) 1

description:
Read counts estimated by using RSEM
rejectP_1


title: wild-type_1_DMSO


title: cultured_oocyte1_class_IV_20_percent_O2_RRBS

value: C57BL/6 Barb

tag: tissue


title: cultured_oocyte1_class_II_20_percent_O2_RRBS

value: oocytes

tag: treatment


title: 88B

status: Public on Jul 07 2021

city: Rotterdam

first: Anton

middle: W

last: Langerak

state: Zuid Holland

address: Dr. Molewaterplein 40

department: Immunology

country: Netherlands

institute: ErasmusMC

description: TCR beta chain sequencing from COVID-19 T cells

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive TRB repertoire for each sample was downloaded in .csv format and processed in R (R Core Team,  2020) during further analysis. Clonotypes below 50 reads were excluded from clustering to reduce the influence of technical sequencing errors. Clustering was performed using the TEIRESIAS algorithm.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited tekst file containing: sample, QC.status, scenario, rearrangements, raw.count, w.junction.count, w.junction.percent, artefacts.count, artefacts.percent, usable.count, usable.percent, w.most.pop.cln.s..count, w.most.pop.cln.s..percent, uniq.usable.seq.count, clonotypes.count, diversity..norm.ed..count, effective.species.count, R1.Q.mean.stdev.count, R2.Q.mean.stdev.count, joined.normally.count, joined.normally.percent, joined.loosely.count, joined.loosely.percent, total.joined.count, total.joined.percent, saved.from.unjoined.count, saved.from.unjoined.percent, low.quality..ee.nt...0.01..count, low.quality..ee.nt...0.01..percent, short...50nt..count, short...50nt..percent, annotated.count, annotated.percent, w.TR.receptor.count, w.TR.receptor.percent, w.B.chain.count, w.B.chain.percent, w.VJ.Vb..Db..Jb.count, w.VJ.Vb..Db..Jb.percent, w.VJ.Vb..Db..Jb.cln

source_name: Whole blood leukocytes_Severe

growth_protocol: Whole blood (WB) samples were collected at multiple instances during the entire hospitalization period and stored at -80 °C until further analysis

extract_protocol:
Total cellular DNA was isolated from whole blood and 1000 ng was amplified through multiplex PCR of TRBV-TRBD-TRBJ gene rearrangements following the BIOMED-2 protocol. PCR products were gel-purified (QIAGEN, Hilden, Germany)
Library preparation was performed according to the manufacturer’s instructions (NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, NEB, Ipswich, MA, USA). The purity and size estimation of the libraries was assessed on an Agilent Bioanalyzer using the Agilent High Sensitivity DNA kit (Agilent Technologies, Lexington, MA, USA). The dsDNA HS Assay Kit was employed for quantification of the sequencing libraries on a Qubit 3.0 fluorometer (ThermoFisher Scientific, Waltham, MA, USA). Paired-end sequencing was performed using the MiSeq Reagent Kit v2 (2x250bp) on the MiSeq Benchtop Sequencer (Illumina, San Diego, CA, USA). PhiX was spiked-in at a 20% concentration to increase library diversity.

value: Yes

tag: disease status

value: Severe

value: Whole blood

value: Whole blood Leukocytes


title: 86B


title: 83B

source_name: Whole blood leukocytes_Critical

value: Critical


title: 87B


title: 85A


title: 86A


title: 84A


title: WTVI_3

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 3 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: Vastus_intermedius_17 mo_wildtype

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: We generated mice in which the Grsf1 gene was selectively ablated in skeletal muscle.  We imported heterozygous Grsf1 mutant mice (Grsf1tm1a) from the European Mouse Mutant Archive (EMMA), in which a LacZ cassette, a Neo cassette, 2 FRT (flippase recognition target) sites, and 3 LoxP (locus of X-over P1) sites were inserted into a Grsf1 allele.  We  removed the LacZ and Neo cassettes by crossing the Grsf1tm1a mice with FLPo mice.  In the resulting Grsf1-LoxP mice, exons IV and V of Grsf1 were floxed.  The Grsf1-floxed mice were further crossed with Myf5Cre mice to generate skeletal muscle-specific Grsf1 knockout (Grsf1cKO) mice.

extract_protocol: Total RNA was isolated from frozen VI muscles from three 17 month old Grsf1cKO and three wildtype control mice using Trizol (Ambion, 15596-026) and the Purelink RNA mini kit (Ambion, 12183018A) followed by on-column Purelink DNase treatment (Ambion, 12185-010).  RNA concentration and quality was measured by Nanodrop (ThermoFisher, Waltham, MA USA) and on the Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

tag: Sex

value: M

tag: age

value: 17  months

value: Wildtype

value: muscle; vastus intermedius


title: ALT301_normal growth-rep3

city: Kurashiki

first: Yoshiyuki

last: Tsuchiya

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA samples were fragmented at 60°C for 30 minutes and hybridized on to Agilent Tobacco Oligo DNA Microarray (4 × 44k, AMADID: 021113). Hybridization was carried out in a incubation chamber at 65°C for 17 hours.

scan_protocol: The slide was scanned at a resolution of 5 µm using an Agilent Microarray Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: The scanned images were analyzed using Feature Extraction Software (Agilent Technologies). To analyze image and signal intensity, raw data of the scanning were processed with the software GeneSpring GX 10 (Agilent Technologies), and normalized to shift to the 75 percentile.

organism: Nicotiana tabacum

source_name: cell, Al-trelant ALT301, normal condition, replication3

label_protocol: The cDNA was synthesized from 200 ng each of total RNA samples; the cRNA was subsequently labelled with Cy3 fluorescent dye using the Low Input Quick Amp Labeling Kit, One-color (Agilent Technologies), following the manufacturer’s instructions. The cRNA target solution was prepared after labelled cRNA was purified using RNeasy mini spin columns (Qiagen).

growth_protocol: The suspension-cultured tobacco cell lines were grown in an Erlenmeyer flask on a rotary shaker operated at 100 rpm at 25°C in the dark.

extract_protocol: The total RNA from cells was extracted using RNeasy Plant Mini Kit (Qiagen) with DNase treatment following the manufacturer's instructions.

treatment_protocol: Tobacco cells were cultured in a modified version of Murashige-Skoog medium.

tag: cell line

tag: genotype/variation

value: Al-trelant

tag: condition

value: normal condition

value: cell culture

tag: growth phase

value: logarithmic-phase


title: 82D


title: 82C


title: 81C


title: 81A


title: WTVI_1_REPEAT


title: 81B


title: WTVI_1


title: 80G


title: ALT301_normal growth-rep2

source_name: cell, Al-trelant ALT301, normal condition, replication2


title: WTVI_2


title: ALT301_normal growth-rep1

source_name: cell, Al-trelant ALT301, normal condition, replication1


title: GRSF1KOVI_1_REPEAT

source_name: Vastus_intermedius_17 mo_Grsf1KO


title: GRSF1KOVI_2


title: 80E


title: SL_normal growth-rep3

source_name: cell, wild-type SL, normal condition, replication3

value: SL

value: wild-type


title: 80F


title: GRSF1KOVI_1


title: SL_normal growth-rep2

source_name: cell, wild-type SL, normal condition, replication2


title: GRSF1KOVI_3


title: SL_normal growth-rep1

source_name: cell, wild-type SL, normal condition, replication1


title: 79C


title: 78A


title: 76D


title: 77D


title: ros1hda6-10.Mnase

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

data_processing:
Reads from MNase-seq were mapped to Arabidopsis genome (Araport11) using Bowtie2 software. Differential nucleosome changes were analyzed using the DANPOS [47]. The alteration of location, fuzziness and occupancy of nucleosomes between samples were calculated using Dpos algorithm and the signal of enriched peaks were analyzed using Dpeak algorithm. The criteria of FDR <0.01 was adopted in MNase-seq data analysis
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: wig format file

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The Arabidopsis seeds from wild-type C24 (WT), ros1–1 mutant, ros1hda6–9 mutant and ros1hda6–10 mutant, were sterilized with 50% bleach containing 0.01% Triton X-100 for 8 minutes, then the seeds were washed 5 times with sterilized ddH2O. The sterilized seeds were sowed on full MS, 3% SUCROSE and 0.6% Agar plates. After 4 days stratification at 4 degree in dark, the seedlings were grown at 16h light/8h dark for 14 days at 21 degree.  The 14-days old seedlings were harvested for genomic DNA, small RNAs and for mono-nucleosome positioning experiments.

extract_protocol: One gram fresh Arabidopsis seedlings from C24, ros1, ros1hda6-9 and ros1hda6-10 were ground to powder with liquid nitrogen, 10ml extraction buffer I (0.44M sucrose, 10mM Tris-HCl, pH8.0, 5mM beta mercaptoethanol, and 1x proteinase inhibitor) were added into the powder, vortex gently to mix the buffer I and plant materials completely. After incubate on ice for 10 minutes, the filtered flow-through was centrifuged at 2880g for 20 minutes. The pellets were resuspended with 10ml Buffer II (0.25M sucrose, 10mM Tris-HCl, pH8.0, 10mM MgCl2, 1% triton X-100, 5mm beta-mercaptoethanol, and 1x proteinase inhibitor), and were incubated on ice for another 10 minutes. After centrifuging at 2100g for 20 minutes, the pellets were re-suspended with 4ml buffer II just without triton X-100 and were centrifuged at 4 degree, 2100xg for 20 minutes. The acquired pellets are nuclei and were resuspended with 4ml percoll resuspension buffer (95% v/v percoll, 0.25M sucrose, 10mM Tris-HCl, pH8.0, 5mm MgCl2, 10mM beta-mercaptoethanol, and 1x proteinase inhibitor). The resuspended nuclei were centrifuged at 4 degree, 12000xg for 10 minutes. The upper phases were removed to a new tube, further diluted at least  five times with nuclei suspension buffer (10% glycerol, 50mM Tris-HCl, pH8.0, 5mM MgCl2, 10mM beta-mercaptoethnol, and 1x proteinase inhibitor), the diluted nuclei were centrifuged at 12000xg for 10 minutes. After centrifugation, the pellets were resuspended with 4ml nuclei suspension buffer and centrifuged again at 12000xg for 10 minutes. The above resuspension and centrifugation were repeated twice more.  Finally, dissolve the pellets with 500ul 1x MNase Buffer with 0.1ug/ul BSA respectively and aliquote 100ul to each new tube, and digested with 0.5ul MNase I (1000 gel unit, NEB) at 37 degree for 20 minutes. To terminate the digestion reaction, 10ul of 0.5M EDTA, 20ul of 1M Tris-HCl (pH 6.8), and 1.5ul of 14mg/ml proteinase K were added into the reaction solution, incubated at 45 degree for another 1 hour. After 1 hour incubation, 1 volume Phenol:Chloroform:Isoamyl (25:24:1) were added and mix well by vigorously shaking for 30 seconds. The mixture was applied to prepared phase locked gel, after centrifuging at 15400xg for 5 minutes, the aqueous phase was removed into new tubes and DNA were precipitated with 1/10 volume of NaOAc, three times of 100% ethanol, and 1ul glycogen. The purified DNA were loaded into 1.5% agarose gel, and the lowest bands equals to around 147bp were excised and purified, and subjected to Illumina library preparation, the prepared libraries were run on Hiseq2000 platform.

value: seedlings

value: 14-days old


title: ros1hda6-9.Mnase


title: C24.MNase


title: 76C

value: Yes


title: ros1hda6-10.sRNAseq

data_processing:
Low quality reads and adapter sequences were removed using TrimGalore [48]. Then we merged the reads in a pair by FLASH [49]. The 18-35 nucleotides clean reads were mapped against the Arabidopsis reference genome (Araport11) using bowtie [50] without mismatch (-v 0 -m 1). Only the unique mapped reads were extracted for further analysis. BEDtools [51] were used for counting the distribution pattern among 21-24nt siRNAs.
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: wig format file

extract_protocol: For small RNA sequencing, total RNAs from C24, ros1, ros1hda6-9 and ros1hda6-10 were first extracted with Trizol, the extracted total RNAs were further digested with DNase I (NEB cat#M0303) and further were cleaned up with acidic phenol (cat#:9722) and phase locked gel. The purified total RNA were run on 15% denature PAGE gel with 8M urea. The small RNAs less than 40nt were purified from PAGE gel. The purified small RNAs were subject to Trueseq small RNA sample prep kit. The prepared libraries were run on Hiseq2000 platform.


title: 75C

value: Severe


title: ros1hda6-9.sRNAseq


title: 73F

value: Whole blood


title: 74B

value: Whole blood Leukocytes


title: 74A

value: Critical


title: 73D


title: C24.sRNAseq


title: ros1.sRNAseq


title: 73E


title: ros1hda6-9.Bisulfite

data_processing:
Raw reads were mapped to Arabidopsis reference genome (Araport11) using Bismark v0.14.3 [44] with default parameters. Methylated cytosines and un-methylated cytosines were quantified from aligned sequences using R package "methylKIT" [45] under standard parameters. A 100bp window sliding at 100 bp intervals was applied to identify methylated regions among samples. P-value of methylated level for each methylated region was calculated by Fisher exact test and sliding linear model (SLIM) method [46] was applied to adjust the multiple testing errors. Methylated regions with at least four cytosines with average coverage larger than 4 as well as corrected p-values <0.05 were kept in the subsequent analysis. Regions with methylation difference >40, >25 and >15 were considered as differentially methylated regions (DMR) for CG, CHG, and CHH contexts.
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: wig format file

extract_protocol: The genomic DNAs were isolated from C24, ros1, ros1hda6-9 and ros1hda6-10 with Plant DNeasy Maxi Kit (Qiagen), and 5ug of genomic DNA was first sheared to around 200bp fragments, then the fragmented genomic DNA were subjected to bisulfite conversion with Epitech Bisulfite kit (Qiagen, cat# 59104), the eluted converted DNA fragments were used to construct with illumina DNA sequencing library construction with TruSeq DNA sample preparation kit. The prepared libraries were run with Illumina Hiseq2000.


title: 72B


title: 72D


title: 72E


title: 72C


title: ros1hda6-10.Bisulfite


title: ros1.Bisulfite


title: 71B


title: 71A


title: ros1.Mnase


title: 70E


title: 76B


title: C24.Bisulfite


title: 70C


title: 69B


title: 72_lib_01444AAC_CTTGTA

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description: Loratadine+Rapamycin C1R

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the mouse genome using STAR (version 2.4.0f1)
The SAM/BAM files were further processed using the SAMtools (version 0.1.18) and read count quantitations were obtained using BEDTools multicov (version 2.25.0).
Gene expression was quantified by as transcripts per million (TPM).
Genome_build: mm9
Supplementary_files_format_and_content: TPM data matrix of gene expression.

source_name: 105K Tsc2-null cancer cells

growth_protocol: Mammary tumors from age-matched immunocompetent mice, fresh frozen -80C.

extract_protocol:
Total RNA from tumor tissue  was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Veheicle (0.2% carboxymethylcellulose (CMC)), rapamycin (0.25 mg/kg/day in CMC; intraperitoneal), loratadine (25 mg/kg/day in CMC; intraperitoneal).

value: Mammary tumor

value: 105K Tsc2-null

value: Loratadine+Rapamycin


title: 71_lib_01443AAC_GGCTAC

description: Loratadine+Rapamycin A3L


title: 68F


title: 70_lib_01442AAC_GATCAG

description: Rapamycin G3L

value: Rapamycin


title: 68E


title: 69_lib_01441AAC_CAGATC

description: Rapamycin D1L


title: 66A


title: 68_lib_01440AAC_GCCAAT

description: Loratadine F3R

value: Loratadine


title: 65D


title: 65E


title: 64C


title: 67_lib_01439AAC_ACAGTG

description: Loratadine B3R


title: 63E


title: 64B


title: 66_lib_01438AAC_TGACCA

description: Vehicle CMC F5L

value: Vehicle


title: 70D


title: 65_lib_01437AAC_CGATGT

description: Vehicle CMC B1L


title: 63D


title: SG_EC3

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

data_processing:
base-calling (Illumina Casava v. 1.8.2)
Illumina quality filtering (custom script)
alignment of reads to the reference genome (TopHat v. 2.0.9)
transcripts assembly and generation of normalized abundance measurements (Cufflinks v. 2.1.1)
Genome_build: Vitis vinifera PN40024 reference genome V1 (assembly 12x). Jaillon O, et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
Supplementary_files_format_and_content: FPKMs

organism: Vitis vinifera

source_name: Embryogenic callus tissue

growth_protocol: Anthers (A) were cultured on a previously described callus induction medium supplemented with 4.5 µM 2,4-dichlorophenoxyacetic acid (2,4-D) and 8.9 μM 6-benzylaminopurine (BAP) (Gribaudo et al., 2004; Gambino et al., 2007). The cultures were maintained at 26 °C in the dark. Three months after the initiation of the culture, calli were transferred for 1 months to embryo proliferation medium (Gribaudo et al., 2004; Gambino et al., 2007) containing 10 µM 2-Napthoxyacetic acid (NOA), 1 μM BAP, 20 µM Indole-3-acetic acid (IAA) and 2.5% activated charcoal. The frequency of callogenesis and embryogenesis for both cultivars was calculated in two consecutive years at 4 months after the initiation of the culture, and calli were classified as embryogenic (EC) or non-embryogenic (NEC) under a stereomicroscope.

extract_protocol:
Total RNA was extracted from approximately 100 mg of anthers, 40d calli, EC and NEC. For each biological replicate, the plant material ground in liquid nitrogen using the tissue lyser system (TissueLyser II, Qiagen), was extracted using the Spectrum Plant Total RNA extraction kit (Sigma Aldrich). The integrity and quantity of RNA were checked with a 2100 Bioanalyzer Chip RNA 7500 series II (Agilent, Santa Clara, CA, USA)) and a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
The anthers, 40d calli, NEC and EC triplicate samples yielded 24 non-directional cDNA libraries, which were prepared from 2.5 µg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego CA, USA) according to the manufacturer’s instructions.

tag: cultivar

value: Sangiovese

tag: embryogenesis aptitude

value: highly competent

value: Embryogenic callus tissue

tag: biological replicate

value: Replicate 3


title: 62F


title: 62E


title: 62D


title: SG_EC2

value: Replicate 2


title: 69C


title: SG_EC1

value: Replicate 1


title: HeLa_siPABPC1&4_48h_5EU_8h_input_NEXTflex_RNA_seq

first: David

last: Bartel

address: 455 Main Street

institute: Whitehead Institute

description:
D18
rRNA depletion with NEBNext rRNA Depletion Kit

data_processing:
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq)

source_name: HeLa cells

growth_protocol: All mammalian cells were cultured at 37°C with 5% CO2. HeLa cells were cultured in DMEM (VWR, 45000-304) with 10% FBS (TaKaRa, 631106). HCT116 OsTIR1 cells were cultured in McCoy’s 5A media (Thermo Fisher, 16600082) supplemented with 10% FBS, 2mM L-glutamine (Thermo Fisher, 25030081). NIH3T3 cells were cultured in DMEM with 10% BCS (Sigma, 12133C).

extract_protocol:
To prepare lysate from mammalian cells, cycloheximide (CHX) was added to each plate at final concentration 100 µg/ml. Plates were immediately moved to a cold room and culture media were removed. Cells were washed twice with ice-cold PBS supplemented with 100 µg/ml CHX. After the last wash, 1 ml buffer RLL (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% (v/v) Triton X-100, 100 µg/ml cycloheximide, 500 unit/ml RNasin Plus (Promega, N2615), 2 mM DTT, cOmplete protease inhibitor cocktail (Sigma, 11836170001, 1 tablet per 10ml buffer)) was added to each 15 cm plate, and cells were scraped off and incubated on ice for 10 min. The resulting lysates were passed through a 26-gauge needle six times and cleared by centrifugation at 1300g at 4°C for 10 min. To prepare lysate from frog oocytes, injected oocytes were washed once with complete OR-2 buffer and three times with buffer RLL. After removing all wash buffer, oocytes were lysed in buffer RLL (10 µl/oocyte) by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5,000g at 4°C for 10 min. One tenth of each cleared lysate was added to 10 volumes of Tri Reagent for total-RNA preparation, following the manufacturer’s protocol. Another small portion (~10 µl) was taken for western analysis. The remainder was aliquoted, flash frozen in liquid nitrogen, and stored at –80°C.
Sequencing libraries were prepared as described previously (Subtelny et al., 2014) and (Eisen et.al, 2020)
Library strategies were as described previously (Subtelny et al., 2014) and (Eisen et.al, 2020)

treatment_protocol: For 5EU labeling: 48 h after siRNA transfection, HeLa cells were incubated with pre-warmed fresh media with 400 µM 5-ethynyl uridine (5EU, Jena Biosciences) for 1, 2, 4, and 8 h. For IAA-indcued degradation, HCT116 cells were incubated with 1 µg/ml doxycycline and 0.2 mM auxinole (Aobious, AOB8812), an inhibitor of OsTIR1 for 6 h, after which fresh media with 1 µg/ml doxycycline and 0.5 mM IAA were added. Cells were collected after 0.5, 1, and 3 h of induction.

value: cell line

tag: Stage

tag: manipulation

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h and incubated with 5-EU for 8h

tag: time after 5eu labeling (h)

tag: time after iaa addition (h)

tag: rna population

value: cytoplasmic RNA, 5-EU pulldown input

tag: library type

value: RNA-seq with NEXTflex kit


title: 62C

value: Yes

value: Severe

tag: tissue

value: Whole blood

tag: cell type

value: Whole blood Leukocytes


title: 68D

tag: disease status


title: 67C


title: CS_EC2

value: Cabernet Sauvignon

value: poorly competent


title: 60C


title: 60E


title: 61A


title: CS_EC3


title: 60B


title: HeLa_siPABPC1&4_48h_5EU_8h_eluate_NEXTflex_RNA_seq

description:
D16
no rRNA depletion

value: cytoplasmic RNA, 5-EU pulldown eluate


title: HeLa_siPABPC1&4_48h_5EU_1h_input_NEXTflex_RNA_seq

description:
D17
rRNA depletion with NEBNext rRNA Depletion Kit

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h and incubated with 5-EU for 1h


title: 59D


title: 59E


title: SG_NEC3

source_name: Not Embryogenic callus tissue

value: Sangiovese

value: highly competent

value: Not Embryogenic callus tissue


title: 58E


title: HeLa_siPABPC1&4_48h_5EU_2h_eluate_NEXTflex_RNA_seq

description:
D14
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h and incubated with 5-EU for 2h


title: HeLa_siPABPC1&4_48h_5EU_4h_eluate_NEXTflex_RNA_seq

description:
D15
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h and incubated with 5-EU for 4h


title: SG_NEC2

value: Replicate 2


title: CS_EC1

value: Embryogenic callus tissue

value: Replicate 1


title: SG_NEC1


title: 58B


title: 57E


title: 58C


title: 56F


title: HeLa_siPABPC1_48h_5EU_8h_input_NEXTflex_RNA_seq

description:
D12
rRNA depletion with NEBNext rRNA Depletion Kit

value: cell line

value: transfected with siRNAs targeting PABPC1 for 48h and incubated with 5-EU for 8h

value: cytoplasmic RNA, 5-EU pulldown input

value: RNA-seq with NEXTflex kit


title: 57D

value: Yes

value: Severe

value: Whole blood

value: Whole blood Leukocytes


title: CS_NEC3

value: Cabernet Sauvignon

value: poorly competent

value: Replicate 3


title: 56D


title: HeLa_siPABPC1&4_48h_5EU_1h_eluate_NEXTflex_RNA_seq

description:
D13
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h and incubated with 5-EU for 1h

value: cytoplasmic RNA, 5-EU pulldown eluate


title: CS_NEC2

value: Not Embryogenic callus tissue


title: 56C


title: 55B

value: Critical


title: CS_NEC1


title: HeLa_siPABPC1_48h_5EU_1h_input_NEXTflex_RNA_seq

description:
D11
rRNA depletion with NEBNext rRNA Depletion Kit

value: transfected with siRNAs targeting PABPC1 for 48h and incubated with 5-EU for 1h


title: 54B


title: 54A


title: 59F


title: HeLa_siPABPC1_48h_5EU_2h_eluate_NEXTflex_RNA_seq

description:
D08
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 for 48h and incubated with 5-EU for 2h


title: 53E


title: SG_40D2

source_name: Undifferentiated callus tissues at 40d of culture

value: Sangiovese

value: highly competent

value: Replicate 2


title: 52A


title: 53D


title: HeLa_siPABPC1_48h_5EU_1h_eluate_NEXTflex_RNA_seq

description:
D07
no rRNA depletion

value: cell line

value: RNA-seq with NEXTflex kit


title: 50A

value: Yes

value: Severe


title: SG_40D1

value: Undifferentiated callus tissues at 40d of culture

value: Replicate 1


title: 51A

value: Whole blood

value: Whole blood Leukocytes


title: CS_40D3

value: Cabernet Sauvignon

value: poorly competent

value: Replicate 3


title: CS_40D2


title: HeLa_siPABPC1_48h_5EU_8h_eluate_NEXTflex_RNA_seq

description:
D10
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 for 48h and incubated with 5-EU for 8h

value: cytoplasmic RNA, 5-EU pulldown eluate


title: HeLa_siControl_48h_5EU_8h_input_NEXTflex_RNA_seq

description:
D06
rRNA depletion with NEBNext rRNA Depletion Kit

value: transfected with non-targeting siRNAs for 48h and incubated with 5-EU for 8h

value: cytoplasmic RNA, 5-EU pulldown input


title: 49A


title: 49B


title: HeLa_siPABPC1_48h_5EU_4h_eluate_NEXTflex_RNA_seq

description:
D09
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 for 48h and incubated with 5-EU for 4h


title: HeLa_siControl_48h_5EU_1h_input_NEXTflex_RNA_seq

description:
D05
rRNA depletion with NEBNext rRNA Depletion Kit

value: transfected with non-targeting siRNAs for 48h and incubated with 5-EU for 1h


title: HeLa_siControl_48h_5EU_8h_eluate_NEXTflex_RNA_seq

description:
D04
no rRNA depletion

value: cell line


title: CS_40D1


title: SG_A3

source_name: Anthers excised from immature flowers

value: Sangiovese

value: highly competent

value: Anthers excised from immature flowers


title: 48A

value: Yes

value: Critical


title: 53F

source_name: Whole blood leukocytes_Severe

value: Severe

value: Whole blood


title: SG_40D3

value: Undifferentiated callus tissues at 40d of culture


title: 47B

value: Whole blood Leukocytes


title: 46C


title: 46B


title: HeLa_siControl_48h_5EU_2h_eluate_NEXTflex_RNA_seq

description:
D02
no rRNA depletion

value: transfected with non-targeting siRNAs for 48h and incubated with 5-EU for 2h

value: RNA-seq with NEXTflex kit


title: HeLa_siControl_48h_5EU_4h_eluate_NEXTflex_RNA_seq

description:
D03
no rRNA depletion

value: transfected with non-targeting siRNAs for 48h and incubated with 5-EU for 4h

value: cytoplasmic RNA, 5-EU pulldown eluate


title: 45A


title: 44A


title: SG_A2

value: Replicate 2


title: 43A


title: SG_A1

value: Replicate 1


title: HeLa_siControl_48h_5EU_1h_eluate_NEXTflex_RNA_seq

description:
D01
no rRNA depletion

value: transfected with non-targeting siRNAs for 48h and incubated with 5-EU for 1h


title: 42A


title: 40A


title: CS_A3

value: Cabernet Sauvignon

value: poorly competent

value: Replicate 3


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_1h_PAL_seq

description:
C27
no rRNA depletion

data_processing:
Library strategy: PAL-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq); *hits.txt files are raw signal intensities from Hiseq 2000 sequencing which are used with a custom algorithm to call poly(A) tail lengths

source_name: HCT116 cells, OsTIR1 knock-in, AID-tagged PABPC1

value: cell line

value: IAA for 1 h

value: cytoplasmic RNA

value: PAL-seq v4


title: 41B

source_name: Whole blood leukocytes_Critical

value: Yes

value: Critical

value: Whole blood


title: 39A

value: Severe

value: Whole blood Leukocytes


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_3h_PAL_seq

description:
C28
no rRNA depletion

value: IAA for 3 h


title: CS_A2

value: Anthers excised from immature flowers


title: 38B


title: RR0542663.051820.TC#1

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Tconvs were magnetically isolated from thawed PBMCs as CD4+CD25neg

data_processing:
Reads were mapped to the human reference genome (GRCh38) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (v27)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

source_name: CD4 Tconv Cell

extract_protocol:
Human Tregs and Tconvs from COVID-19 patients and healthy donors were magnetically isolated from frozen PBMCs using a Stem Cell kit, as CD4+CD25hiCD127lo and CD4+CD25–, respectively. Around 1,000 isolated cells were directly into lysis buffer for RNA-seq (Smart-seq2)  library preparation following the standard ImmGen low-input protocol (www.immgen.org). Samples were collected and sequenced in two cohorts.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

tag: disease

value: Blood

tag: processing batch

tag: severity

value: Recovered

tag: donor

value: CD4 Tconv Cell


title: 36A


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_30m_PAL_seq

description:
C26
no rRNA depletion

value: IAA for 0.5 h


title: RR0509389.051920.TC#1


title: 36B


title: HeLa_RPL3_3xHA_siPABPC1&4_48h_PAL_seq

description:
C23
no rRNA depletion

source_name: HeLa cells, T-Rex, Flp-In with RPL3 3xHA, OsTIR1 knock-in

value: transfected with siRNAs targeting PABPC1 abd PABPC4 for 48h

value: PAL-seq v3


title: 33A


title: 38A


title: HCT116_OsTIR1_PABPC1_AID_minus_IAA_PAL_seq

description:
C25
no rRNA depletion

value: cell line

value: no IAA


title: HeLa_RPL3_3xHA_siPABPC1&4_siTUT4&7_48h_PAL_seq

description:
C24
no rRNA depletion

value: transfected with siRNAs targeting PABPC1, PABPC4, TUT4 and TUT7 for 48h

value: cytoplasmic RNA


title: 42B

value: Yes


title: CS_A1

value: Cabernet Sauvignon

value: poorly competent

value: Replicate 1


title: 34A

value: Critical

value: Whole blood

value: Whole blood Leukocytes


title: HeLa_RPL3_3xHA_siPABPC1_siTUT4&7_48h_PAL_seq

description:
C22
no rRNA depletion

value: transfected with siRNAs targeting PABPC1, TUT4 and TUT7 for 48h


title: 32B


title: 35A


title: HeLa_RPL3_3xHA_siPABPC1_48h_PAL_seq

description:
C21
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 for 48h


title: 37B

value: Severe


title: 31A


title: RR0931294.060520.TC#1

value: Blood

value: Recovered

value: CD4 Tconv Cell


title: 30B


title: 28B


title: HeLa_RPL3_3xHA_siControl_48h_PAL_seq

description:
C20
no rRNA depletion

value: cell line

value: transfected with non-targeting siRNAs for 48h

value: PAL-seq v3


title: 29A


title: RR0370807.042120.TC#1


title: HeLa_siPABPC1&4_72h_rep2_TAIL_seq

description:
C17
no rRNA depletion

data_processing:
Library strategy: TAIL-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq); *hits.txt files are raw signal intensities from Hiseq 2000 sequencing which are used with a custom algorithm to call poly(A) tail lengths

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 72h

value: cytoplasmic RNA

value: TAIL-seq


title: RR0243818.071420.TC#1


title: RR0306970.042120.TC#1


title: 26A

value: Yes


title: 27A


title: 25B


title: 37A


title: HeLa_siPABPC1&4_72h_TAIL_seq

description:
C16
no rRNA depletion


title: HeLa_siPABPC4_72h_TAIL_seq

description:
C15
no rRNA depletion

value: transfected with siRNAs targeting PABPC4 for 72h


title: RR0941834.072320.TC#1


title: RR0941176.041720.TC#1


title: 24A

value: Critical


title: 23A

value: Whole blood


title: 22A

value: Whole blood Leukocytes


title: 21B


title: RR0857858.042720.TC#1


title: 21A


title: 32A


title: HeLa_siControl_72h_TAIL_seq

description:
C13
no rRNA depletion

value: transfected with non-targeting siRNAs for 72h


title: 20A


title: 19A


title: 18B


title: RR0823855.041320.TC#1


title: RR0830593.041320.TC#1


title: 17C


title: RR0234740.072320.TC#1


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_1h_ribo_seq

description:
B15
rRNA depletion with custom oligos

data_processing:
Library strategy: ribo-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq)

value: IAA for 1 h

value: ribo-seq (ribosome footprint profiling)


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_3h_ribo_seq

description:
B16
rRNA depletion with custom oligos

value: IAA for 3 h


title: 18A


title: 16C


title: RR0907841.051820.TC#1

value: Blood

value: Recovered


title: RR0997256.051220.TC#1

value: CD4 Tconv Cell


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_30m_ribo_seq

description:
B14
rRNA depletion with custom oligos

value: cell line

value: IAA for 0.5 h


title: 14A


title: 14B


title: 15A


title: HCT116_OsTIR1_PABPC1_AID_minus_IAA_ribo_seq

description:
B13
rRNA depletion with custom oligos

value: no IAA


title: 13A


title: 12A


title: HeLa_siPABPC1_72h_TAIL_seq

description:
C14
no rRNA depletion

value: transfected with siRNAs targeting PABPC1 for 72h

value: cytoplasmic RNA


title: RR0157115.051220.TC#1


title: HeLa_siPABPC4_48h_ribo_seq_with_mito_ribosomes

description:
B11
rRNA depletion with custom oligos

value: transfected with non-targeting siRNAs for 48h


title: 11A

value: Yes


title: RR0614457.051920.TC#1


title: HeLa_siPABPC1&4_48h_ribo_seq_with_mito_ribosomes

description:
B12
rRNA depletion with custom oligos

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h


title: RR0656234.050720.TC#1


title: 10A

value: Critical

value: Whole blood


title: 10B

value: Whole blood Leukocytes


title: HeLa_siPABPC1&4_72h_ribo_seq

description:
B10
rRNA depletion with custom oligos

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 72h


title: 9A


title: RR0469109.051920.TC#1


title: 8A


title: RR0424088.041520.TC#1

value: mild outpatients


title: 7F


title: 7E


title: HeLa_siPABPC1_72h_ribo_seq

description:
B08
rRNA depletion with custom oligos

value: ribo-seq (ribosome footprint profiling)


title: RR0615993.052220.TC#1

value: Blood


title: 7D


title: 7C


title: RR0602232.050120.TC#1


title: 6F


title: RR0467460.050520.TC#1


title: 6D


title: 5E


title: 5C


title: 5D


title: RR0248668.050520.TC#1


title: 4G


title: HeLa_siControl_72h_ribo_seq

description:
B07
rRNA depletion with custom oligos

value: transfected with non-targeting siRNAs for 72h


title: RR0736447.041020.TC#1

value: hospitalized moderate to severe

value: CD4 Tconv Cell


title: RR0378574.050720.TC#1


title: 5B


title: 4E


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_1h_RNA_seq

description:
A16
rRNA depletion with NEBNext rRNA Depletion Kit

value: cell line

value: IAA for 1 h

value: ribo-seq matched RNA-seq


title: HCT116_OsTIR1_PABPC1_AID_minus_IAA_RNA_seq

description:
A14
rRNA depletion with NEBNext rRNA Depletion Kit

value: no IAA

value: cytoplasmic RNA


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_30m_RNA_seq

description:
A15
rRNA depletion with NEBNext rRNA Depletion Kit

value: IAA for 0.5 h


title: HCT116_OsTIR1_PABPC1_AID_plus_IAA_3h_RNA_seq

description:
A17
rRNA depletion with NEBNext rRNA Depletion Kit

value: IAA for 3 h


title: HeLa_siPABPC4_72h_ribo_seq

description:
B09
rRNA depletion with custom oligos

value: transfected with siRNAs targeting PABPC4 for 72h


title: HeLa_siPABPC1&4_48h_NEBNext_RNA_seq

description:
A13
rRNA depletion with NEBNext rRNA Depletion Kit

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 48h


title: 3E

value: Yes

value: Critical

value: Whole blood

value: Whole blood Leukocytes


title: 2G


title: HeLa_siControl_48h_NEBNext_RNA_seq

description:
A12
rRNA depletion with NEBNext rRNA Depletion Kit

value: transfected with non-targeting siRNAs for 48h


title: 2F


title: RR0318907.051220.TC#1

value: Blood


title: 2E


title: 2D


title: RR0183111.051520.TC#1

value: hospitalized moderate to severe


title: HeLa_siPABPC1&4_72h_RNA_seq

description:
A11
rRNA depletion with RiboZero Gold kit

value: transfected with siRNAs targeting PABPC1 and PABPC4 for 72h


title: HeLa_siPABPC4_72h_RNA_seq

description:
A10
rRNA depletion with RiboZero Gold kit

value: cell line


title: 2C


title: 4F


title: 1G


title: RR0915093.033120.TC#1

value: CD4 Tconv Cell


title: 1F


title: HeLa_siPABPC1_72h_RNA_seq

description:
A09
rRNA depletion with RiboZero Gold kit

value: transfected with siRNAs targeting PABPC1 for 72h

value: ribo-seq matched RNA-seq


title: RR0866687.050720.TC#1


title: 3G

description: TCR beta chain sequencing from COVID-19 T cells


title: 1E


title: HeLa_siControl_72h_RNA_seq

description:
A08
rRNA depletion with RiboZero Gold kit

value: transfected with non-targeting siRNAs for 72h

value: cytoplasmic RNA


title: RR0511931.040820.TC#1


title: 1B


title: JEV treatment Donor3

city: Faridabad

first: Manjula

last: Kalia

state: Haryana

address: NCR Biotech Science cluster Gurugram-Faridabad Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

description:
Sample 6
Monocytes derived from human PBMCs, then differentiated into MoDCs.
sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx

data_processing:
The pre-processing operations included a quality check and removal of sub-par quality reads (Phred Score <30) was done by FastQC software (version 0.11.9).
Adaptor removal was done by Trim Galore software (Version 0.6.5).
Reads were mapped to GH38 human reference genome using Bowtie2 and Tophat2.1.1.
The expression of the assembled transcriptome was estimated using Cufflinks 2.2.1.
The normalization was performed using FPKM method followed by Log2 transformation of the value.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx: Excel file includes abundance measurements.

source_name: PBMC

growth_protocol: Primary MoDCs derived from healthy donor.

extract_protocol:
Samples in TRIZOL were given for RNA extraction and RNA-Seq analysis. Total RNA samples with RNA Integrity Number (RIN) ≥ 7 were selected for library preparation.
RNA-seq library preparation was performed using TruSeq® RNA library Prep Kit v2 (Illumina).

treatment_protocol: Mock or JEV infection.

tag: diagnosis

value: Healthy

value: Monocytes-derived dendritic cells (MoDCs)

tag: treatment

value: JEV infection


title: RR0524129.050720.TC#1


title: Normal Stretched TPC Hashes

city: Stanford

first: Christopher

last: Still

state: California

address: 443 Via Ortega, Room 376

institute: Stanford

description: Cell Hashing file

data_processing:
10X Chromium libraries processed by Cellranger version 3.0.2.
Drop-seq libraries processed using the Drop-seq alignment cookbook. Hisat2 was used instead of the standard STAR aligner.
Cell hashing data was processed using CITE-seq-Count python package version 1.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Drop-seq processed files are tab-delimited text files
Supplementary_files_format_and_content: Cell hashing processed files are csv files
Supplementary_files_format_and_content: 10X Chromium libraries are contained in standard cellranger output filtered_feature_bc_matrix

organism: synthetic construct

source_name: Antibody coupled oligo

growth_protocol: Following extraction of cells from tendon samples, cells were plated at low density (500 cells per cm^2) until confluent. All cells used in experiments started at passage 2. Cells were grown in low-glucose DMEM with 10% FBS, 50ug/ml ascorbic acid, and antibiotics.

extract_protocol:
Peritendous connective tissue was removed. Tendon tissue was then broken down by digestion with 0.1% type IV collagenase at 37°C with gentle agitation. Cells were then passed through a 70-micron filter to obtain a single cell suspension.
Drop-seq libraries were constructed as detailed in Macosko et al. 2015 with minor exceptions. A glass dolomite chip was used instead of the traditional PDMS chip. 10X Chromium Single Cell 3' V3 libraries were generated according to the standard protocol by the Stanford Functional Genomics Facility (SFGF). Cell Hashing libraries were generated according to the standard protocol by the SFGF.

treatment_protocol: Moderate strength cyclic stetch (6% end-to-end) for 12 hours a day, 3 days in a row followed by 1 day of rest.

tag: hash oligo type

value: TotalSeq -A Hashtags


title: Disease Stretched TPC Hashes

description: Cell Hashing file


title: Mock treatment Donor3

description:
Sample 5
Monocytes derived from human PBMCs, then differentiated into MoDCs.
sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx

value: Mock infection


title: RR0213942.051420.TC#1


title: JEV treatment Donor2

description:
Sample 4
Monocytes derived from human PBMCs, then differentiated into MoDCs.
sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx


title: Metaphase oocytes, rep2, In vitro

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description:
In vitro
5B_

data_processing:
quality filtered and trimmed, and adaptor sequences were removed using  Quality filtering and adaptor removal using trim_galore (v0.4.1)
Mapping to mouse genome (mm10) using Tophat2
featureCounts software was used to quantify the number of reads mapped to each gene using gene annotation from Ensembl release 19
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text table with TPM normalized counts for every gene and every sample

source_name: Metaphase oocytes

growth_protocol: In vivo or in vitro. In vitro: alpha-minimal essential medium (α-MEM, Gibco, UK) supplemented with 10% fetal bovine serum (FBS, Gibco).

extract_protocol:
Arcturus® Paradise® Plus RNA Extraction and Isolation Kit (#KIT0312I Arcturus Bioscience Inc., Mountain View, CA, USA) was used for isolation of total cellular RNA from the microdissected cells on the LCM caps, according to the manufacturer’s protocol. RNA from each cap was pooled for the same oocyte stage during extraction. Total cellular RNA from oocytes collected in vivo and in vitro was isolated using Picopure (#KIT0204 Arcturus Bioscience, Inc., Mountain View, CA, USA).
The Ovation® PICO SL WTA System V2 RNA amplification system (#3312 NuGen, Inc., San Carlos, CA, USA) was used for conversion of isolated RNA from the LCM-derived samples to cDNA and linear amplification. Library preparation for microdissected oocytes was performed using an Illumina TruSeq RNA Access kit at BGI, according to the manufacturer’s protocol. RNA sequencing was performed on an Illumina HiSeq platform with two lanes (5 gb per sample). Library preparation for collected oocytes in both groups was performed using the Smart-seq II method, and RNA sequencing was performed using the Illumina HiSeq platform with one lane (5 gb per sample).

value: Oocytes

tag: strain

value: C57Bl/6j x CBA/J


title: Oocytes from primary follicles, rep3, In vitro

description:
In vitro
1F_

source_name: Oocytes from primary follicles


title: Mock treatment Donor2

description:
Sample 3
Monocytes derived from human PBMCs, then differentiated into MoDCs.
sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx


title: Metaphase oocytes, rep1, In vitro

description:
In vitro
5A_


title: HH0000002.072820.TC#1

value: HD


title: JEV treatment Donor1

description:
Sample 2
Monocytes derived from human PBMCs, then differentiated into MoDCs.
sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx


title: Oocytes from primary follicles, rep1, In vitro

description:
In vitro
1D_


title: Oocytes from primordial follicles, rep3, In vitro

description:
In vitro
1C_

source_name: Oocytes from primordial follicles


title: 1D

value: Yes

value: Critical

value: Whole blood

value: Whole blood Leukocytes


title: 1C


title: RR0611936.010220.TC#1

description: Tconvs were magnetically isolated from thawed PBMCs as CD4+CD25neg

value: Blood

value: CD4 Tconv Cell


title: Mock treatment Donor1

description:
Sample 1
Monocytes derived from human PBMCs, then differentiated into MoDCs.
sample_1_3_5_UN_sample_2_4_6_IN_diff.xlsx


title: RR0849884.051320.TC#1

value: hospitalized moderate to severe


title: Oocytes from primordial follicles, rep1, In vitro

description:
In vitro
1A_


title: RR0890519.012220.TC#1


title: Metaphase oocytes, rep3, in vivo

description:
in vivo
8C_


title: Oocytes from primordial follicles, rep2, In vitro

description:
In vitro
1B_


title: Metaphase oocytes, rep1, in vivo

description:
in vivo
8A_


title: Oocytes from primary follicles, rep3, in vivo

description:
in vivo
4F_


title: RR0947025.020520.TC#1


title: Metaphase oocytes, rep3, In vitro

description:
In vitro
5C_


title: Oocytes from primary follicles, rep2, in vivo

description:
in vivo
4E_


title: Metaphase oocytes, rep2, in vivo

description:
in vivo
8B_


title: AC3034430.110519.TC#1


title: HH0000003.082520.TC#1


title: Oocytes from primary follicles, rep2, In vitro

description:
In vitro
1E_


title: Oocytes from primary follicles, rep1, in vivo

description:
in vivo
4D_


title: RR0865315.021220.TC#1


title: Oocytes from primordial follicles, rep3, in vivo

description:
in vivo
4C_


title: Oocytes from primordial follicles, rep2, in vivo

description:
in vivo
4B_


title: RR0438670.020620.TC#1


title: Oocytes from primordial follicles, rep1, in vivo

description:
in vivo
4A_


title: PFPC4

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

country: South Korea

institute: Inha university hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: HUMAN PD tunica albuginea (TA)

growth_protocol: DMEM contained with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: NF and PF no treatment, PFPC treatment at 1ug/ml for 24 hours.

value: PD tunica albuginea (TA) fibroblasts

tag: agent

value: PC-NVs


title: ATAC-seq_Naive_DOHH_KO_4

city: Baltimore

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description:
processed data file:
Naive_DOHH_KO.bw

data_processing:
Sequenced samples were trimmed with Trimmomatic and mapped using Bowtie2. Only fragments with less than 150bp were kept.
Open chromatin was detected with MACS2, while differences between treatments was determined using DiffBind with at lest 2 fold change in accessibility and a false discovery rate lower than 0.05.
For visualization only, replicate mapped files were merged with SAM tools and coverage files were generated with deepTools and visualized alongside coverage files on IGV.
Bed files were analyzed with Bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files showing normalized filtered mapped reads.

source_name: Spleen and Lymph node

growth_protocol: CD4+ T cells from the spleen and lymph nodes were isolated by negative selection using a Stem Cell kit according to the manufacturers instructions (Stem Cell, Cat: 19852). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 55 μM β- mercaptoethanol. All activations were done with 5 ug/mL anti-CD3 and 2 ug/mL anti- CD28 and 100 U/mL IL-2. TH polarizations were performed as follows: TH1 – 4 μg/mL anti-IL-4, 10 ng/mL IL-12, 10 ng/mL IL-2. TH2 – 4 μg/mL anti-IFN- , 10 ng/mL IL-4, 10 ng/mL IL-2. TH17 – 10 μg/mL anti-IFN- , 10 μg/mL anti-IL-4, 5 ng/mL IL-6, 5 ng/mL TGF- , 10 μg/mL IL-1 . Treg – 4 μg/ mL anti-IFN- , 4 μg/mL anti-IL-4, 10 ng/mL TGF-B, 10 ng/mL IL-2. Cells were analyzed on day 4 of polarization.

extract_protocol:
5x10^4 T cells treated as described were washed in PBS and then lysed in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630 (all Sigma). Nuclei were then spun down and then resuspend in 25 l TD (2x reaction buffer), 2.5 L TDE1 (Nextera Tn5 Transposase) and 22.5 L nuclease-free water, incubated for 30 min at 37°C. DNA was purified with the Qiagen MinElute PCR Purification Kit (Thermo Fisher Scientific).
Libraries were prepared using the Nextera DNA library Prep Kit (Illumina) adapting a published protocol (Buenrostro et al., 2015). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol.

treatment_protocol: CD4 T cells were isolated from the spleen and lymphnode of mice expressing Cre recombinase (CD4Cre) under the control of the CD4 promoter crossed with Dohh flox/flox and Odc flox/flox mice.

value: Spleen and Lymph node

value: CD4 T cell

tag: genotype

tag: polarization

value: Naive


title: ATAC-seq_Naive_DOHH_WT_4

description:
processed data file:
Naive_DOHH_WT.bw


title: RR0542663.051820.TR#1

description: Tregs were magnetically isolated from thawed PBMCs as CD4+CD25hiCD127lo

source_name: CD4 TReg Cell

value: Recovered

value: CD4 TReg Cell


title: PFPC1


title: ATAC-seq_TH2_ODC_WT_3

description:
processed data file:
TH2_ODC_WT.bw


title: PFPC2


title: RR0306970.042120.TR#1


title: RR0941834.072320.TR#1


title: RR0509389.051920.TR#1


title: PF4


title: ATAC-seq_TH17_ODC_WT_3

description:
processed data file:
TH17_ODC_WT.bw


title: ATAC-seq_TH1_ODC_WT_3

description:
processed data file:
TH1_ODC_WT.bw