title: ATP1_M

value: Placenta

tag: strain

tag: developmental stage


title: H. burtonii YPD + 1M KCl 1hr #2

status: Public on Dec 01 2021

type: SRA

city: Seoul

first: Dong Wook

last: Lee

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang university

library_source: transcriptomic

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 Hyphopichia burtonii whole genome using Tophat
FPKM calculation using cufflinks.
Genome_build: Hyphopichia burtonii (NCBI ASM385679v1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Hyphopichia burtonii

source_name: H. burtonii YPD + 1M KCl 1hr

growth_protocol: precultured wildtype H. burtonii was inoculated in YPD and supplemented YPD broth at OD600 = 0.6 and culture 1 hour

extract_protocol:
After culture, OD 5 of samples were harvested and total RNA were extracted RNA preparation method following DOI: 10.1016/j.ab.2019.113408 paper
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA-Seq Library Prep Kit standard protocols.

tag: isolation source

value: Nuruk

tag: genotype/variation

value: WT

tag: treatment

value: YPD + 1M KCl 1hr


title: Kelly_1003-2

city: Darlinghurst

first: Niantao

last: Deng

state: NSW

address: 384 Victoria Street

department: Cancer Theme

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Star alignment
RSEW raw counts
Genome_build: hg19
Supplementary_files_format_and_content: txt

organism: Homo sapiens

source_name: Kelly cell line

growth_protocol: 6x10^5 Kelly cells were seeded in 6 well plates. Kelly media: Roswell Park Memorial Institute (RPMI) medium (Gibco) supplemented with 10% Fetal Bovine Serum (FBS) (Hyclone)

extract_protocol:
RNA was extracted using the Qiagen miRNeasy mini kit (Qiagen). RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies) and integrity verified using an Agilent Bioanalyser 2100 with the 6000 Nano Assay (Agilent Technologies).
Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina) with 1 μg of input RNA.

treatment_protocol: Cells were reverse transfected with 25 nM microRNA mimics (Dharmacon) with Dharmafect 1 Transfection reagent. The following day the media was changed. 48 hour after transfection cell pellets were harvested for RNA extraction.

tag: cell line

value: Kelly

tag: cell type

value: neuroblastoma

tag: miRNA mimic


title: H. burtonii YPD + 1M NaCl 1hr #2

source_name: H. burtonii YPD + 1M NaCl 1hr

value: YPD + 1M NaCl 1hr


title: ATF6_F

city: Melbourne

first: Thi

middle: Thanh Mai

last: Truong

state: VIC

address: Gate 12 Royal Parade, Parkville

department: BioSciences

institute: The University of Melbourne

description:
DESeq2_In_vivo_Liver_vs._AOX_Liver.txt
DESeq2_Control_Liver_vs._AOX_Liver.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of  raw FASTQ data files was assessed with FastQC
Trim Galore! was used to trim the 13 bp of Illumina standard adapters from the ends of reads.
Reads were aligned to the UCSC GRCm38.98/mm10 reference genome with RNA STAR
featureCounts was used to measure gene expression as counted reads
DESeq2 was used to identify differentially expressed genes (DEGs) and their fold changes from count data.
Genome_build: UCSC GRCm38.98/mm10
Supplementary_files_format_and_content: DESeq2 txt/tabular files contain Ensembl Gene IDs (ENSG), mean normalised counts, log2(fold change), standard error of the log2(fold change), Wald statistic, p-value, and p-value adjusted with the Benjamini-Hochberg procedure which controls false discovery rate (FDR), for each gene

organism: Mus musculus

source_name: Murine 14.5 Liver

growth_protocol: Embryos were collected from superovulated female mice and cultured in G series media supplemented with or without antioxidants. Embryos were also collected from superovulated female mice and cultured in G series media then vitrified and thawed with or without antioxidants. Alternatively, in vivo derived embryos were flushed from uteri on day 4. D4 blastocysts were transferred to the uteri of pseudopregnant female mice and allowed to grow for a further 10 days. Fetuses and placentas were collect on E14.5 and tissues harvested for RNA extraction

extract_protocol:
Fetuses and accompanying placentae were removed from uterine horns, flash frozen on dry ice, and RNA was harvested using a Qiagen RNeasy Plus Mini Kit. RNA was analysed on the Illumina HiSeq 2500 system at the Australian Genome Research Facility (AGRF)  with 1 ug of total RNA as input for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos (and resultant fetal tissues designated treatment) were cultured in G series media supplemenented with a combination of antioxidants (alpha-lipoic acid, N-acetly-L-cysteine and L-carnitine) for the duration of the culture period. Control embryos were cultured in G series media containing no antioxidants. For vitrification groups embryos were collected from superovulated female mice and cultured in G series media then vitrified and thawed with or without antioxidants.

tag: tissue

value: Liver

value: C57BL/6 x CBA F1

value: In vitro treated

tag: Sex

value: Female


title: H. burtonii YPD 1hr #2

source_name: H. burtonii YPD 1hr

value: YPD 1hr


title: SCI_EtOH_24h_duplicate2

type: RNA

city: Taipei

first: Yuan-Chii

middle: G.

address: 250, Wuxing Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

description: Gene Expression data

hyb_protocol: According to the Affymetrix manufactor's manual.

data_processing: The data are normalized using RMA in GeneSpring GX 10.

label: biotin

organism: Rattus norvegicus

source_name: spinal cord  with injury, EtOH, 24h

growth_protocol: Long Evans female rats (8 or 9 week-old) were purchased from National Laboratory Animal Center, Taipei, Taiwan. All animals were housed in a 12-h light/dark cycle and had free access to water and food all the time. For animal care and surgical procedures, we followed the National Institutes of Health Guide for the Care and Use of Laboratory Animals (NIH Publications No. 80-23, revised 1978) and all surgical protocols were approved by the Animal Care and Use Committee of Taipei Medical University.

extract_protocol: Following different time after MP, EPO or control medication, SCI animals were anesthetized with a mixture of Zoletil 50 and Rompun described earlier and the 5-mm lesion spinal cord was removed, frozen immediately in liquid nitrogen and stored in liquid nitrogen prior to RNA extraction. Total RNA was extracted by the Trizol method and the integrity of RNA was examined by Agilent Bioanalyzer (Agilent Technologies, Inc. Headquarters, Palo Alto, CA, USA) before oligo microarray analysis started.

treatment_protocol: In MP experiment, animals were randomly assigned into four groups: spinal cord injury with 70% ethanol (SCI + EtOH), spinal cord injury with MP (30 mg/kg) (SCI + MP), Sham + EtOH and Sham + MP. In EPO experiment, animals were randomly assigned into four groups: spinal cord injury with H2O (SCI + H2O), spinal cord injury with EPO (5000 U/kg) (SCI + EPO), Sham + H2O and Sham + EPO. Animals were sacrificed at 2, 4, 6, 8, 12, 24 and 48 hours after medication. Additional animals including Sham + EtOH, SCI + EtOH, Sham + H2O, and SCI + H2O were sacrificed immediately after control medication. For all surgeries, animals were anesthetized by a mixture of Zoletil 50 (25 mg/kg) and Rompun (xylazine, 10 mg/Kg) via intraperitoneal injections.

tag: injury

value: SCI

tag: medication

value: EtOH

tag: time


title: Kelly_Sc-1

value: Scrambled control


title: ATF5_F


title: SCI_EtOH_48h_duplicate1

description: Gene Expression data

scan_protocol: According to the Affymetrix manufactor's manual.

source_name: spinal cord  with injury, EtOH, 48h


title: ATF4_F


title: H. burtonii YPD + 1M sorbitol 1hr #1

source_name: H. burtonii YPD + 1M sorbitol 1hr

value: YPD + 1M sorbitol 1hr


title: libr95_human_TH_plus_hiPSC1

city: Bethesda

first: Xylena

last: Reed

state: MD

address: 35 Convent Dr. bldg 35 Rm1A1015

department: National Institute on Aging

country: USA

institute: NIH

data_processing:
Standard built in Illumina Bustard software was used for base calling
Data filtering was based upon quality scores, and quality scores over read cycles was calculated using picard-tools
Transcript abundance was quantified using Salmon in a non-alignment-based mode
Gene level counts were estimated using tximport package
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Gene level counts

source_name: FACS TH-positive dopaminergic neurons

growth_protocol: iPS cells were differentiated in Serum Reduced Media (SRM) base made with Knockout DMEM/F-12  with Knockout Serum Replacement , 1x GlutaMAX, 1x NEAA and 0.055 mM 2-mercaptoethanol supplemented with 100 nM LDN193189 and 10 µM SB431542 to start neural differentiation at day 0. For the next two days 100 ng/ml SHH, 2 µM puromorphamine and 100 ng/ml FGF8b were added to the previous media to signal dopaminergic specification. On days three and four 3 µM CHIR99021 was added to the supplemented media. Base media was gradually shifted from SRM to neural media (Neurobasal with 1x GlutaMAX, 1x Penicillin-Streptomycin, 1x N2 supplement and 1x B-27 without retinoic acid) between days five and ten. SB431542 was removed from the base media on day five; FGF8b and puromorphamine were removed on day seven. On day 11 SHH and LDN193189 were removed and the base media was completely shifted to NB/B-27 base media (Neurobasal with 1x P/S and 1x B-27 without retinoic acid) and additional growth factors, 20 ng/ml BDNF, 0.2 mM Ascorbic Acid, 20 ng/ml GDNF, 1 mM cAMP, 1 ng/ml TGF-beta3 and 10 µM DAPT were added daily. On day 13 CHIR99021 was removed from the supplements and the media continued to be changed daily with the remaining supplements until day 28 when cells were collected.

extract_protocol:
Total RNA was collected using a standard TRIzol reagent protocol
1ug total RNA underwent library preparation using the TruSeq Stranded Total RNA Library prep kit with rRNA removal mix Gold (Illumina)

tag: donor line

tag: tissue/cell type

value: FACS TH-positive dopaminergic neurons


title: SCI_EtOH_48h_duplicate2

description: Gene Expression data

label_protocol: According to the Affymetrix manufactor's manual.


title: SCI_EtOH_24h_duplicate1

description: Gene Expression data


title: H. burtonii YPD + 1M KCl 1hr #1


title: ATF3_M

value: Male


title: SCI_EtOH_12h_duplicate1

description: Gene Expression data

source_name: spinal cord  with injury, EtOH, 12h


title: SCI_EtOH_8h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, EtOH, 8h


title: ATF2_M


title: H. burtonii YPD + 1M NaCl 1hr #1

value: Nuruk


title: libr82_human_iAstr_WT4

source_name: iAstrocytes

growth_protocol: iPSC were split using StemPro Accutase cell dissociation reagent and 0.2 x 106 cells were seeded on matrigel coated plates. iPSCs were differentiated into neuronal stem cells (NSCs) by growing them to a confluent monolayer for 7 days in Neural Induction Media. NIM was replaced on days 1, 3, 5, 6 and 7. NSCs were then expanded and passaged twice using Accutase in the presence of Y-27632 dihydrochloride at 1:4-1:6 ratio on matrigel coated plates in Neuronal Expansion Media (NEM, 1:1 Neurobasal and Advanced DMEM/F-12 with 1x Neural Induction Supplement). NEM was replaced every other day before differentiating the NSC into astrocytes. For the final differentiation to astrocytes, NSCs were seeded on matrigel coated plates and differentiated in Astrocyte Differentiation Media (ADM, DMEM with 1% FBS and 1x N2 supplement). ADM was replaced every 2-3 days for 48 days and cells were split 1:4-1:6 for expansion upon reaching confluency until RNA was collected.

value: iAstrocytes


title: SCI_EtOH_8h_duplicate1

description: Gene Expression data


title: H. burtonii YPD 1hr #1

value: WT


title: ATF1_M


title: libr80_human_iAstr_WT2


title: Foxp3EGFPCre Treg , 3

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

description: C

data_processing:
fastq file to bam file to count file Rsubread (feature Counts) Default parameters
Count file to Gene differential expression file edgeR (version 3.28)  Default parameters
Count file to Gene differential expression file DESeq2 (version 1.26.0)  Default parameters
Count file to Gene differential expression file Lima (version 3.42.2)  Default parameters
Join results Results_RNASeq.xlsx
Genome_build: GRCm38/mm10 (UCSC reference)
Supplementary_files_format_and_content: vcf files and excel file

source_name: spleen

extract_protocol:
The cells were sorted our using Foxp3YFP reporter, then they were lysed using RLT buffer. The RNA was extracted using the Qiagen miniRNasy kit as per manufacturer's protocol
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

treatment_protocol: Tregs were cell sorted in a Sony sorter and Snap Freeze before RNA preparation

value: Foxp3EGFPCre Treg

value: Treg cells


title: SCI_EtOH_6h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, EtOH, 6h


title: libr79_human_iAstr_WT1


title: ACP5_F

description:
DESeq2_In_vivo_Placenta_vs._Control_Placenta.txt
DESeq2_Control_Placenta_vs._AOX_Placenta.txt
DESeq2_In_Vitro_Control_Placenta_ vs._ VIT_Control_Placenta.txt

source_name: Murine 14.5 Placenta

value: Placenta

value: In vitro control


title: Foxp3EGFPCre Treg , 2

description: C


title: SCI_EtOH_4h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, EtOH, 4h


title: libr96_human_TH_minus_hiPSC2

source_name: FACS TH-negative dopaminergic neurons

value: FACS TH-negative dopaminergic neurons


title: ACP4_F

value: C57BL/6 x CBA F1


title: libr59_human_iPSC_dox_neur_WT3

source_name: doxNeurons

growth_protocol: To induce expression of mNGN2, 7 x 105 iPSC were seeded on matrigel-coated plates in induction medium (DMEM/F12, 1x NEAA, 1x L-glutamine, 1x N2 Supplement, supplemented with 10 nM Y-27632 dihydrochloride and 2 µg/mL doxycycline hydrochloride. Media was changed daily with induction medium supplemented with 2 µg/mL doxycycline hydrochloride. After three days, pre-differentiated cells 2 x 105 iPSC were re-seeded on poly-L-ornithine coated plates in Cortical Neuron Culture Medium (BrainPhys medium, 1x B-27 Supplement, 10 ng/mL NT-3, 10 ng/mL BDNF, 1 µg/mL Mouse Laminin). Half of the media was replaced with fresh Cortical Neuronal Culture Medium 4 days after plating and RNA was isolated 3 days later.

value: doxNeurons


title: libr58_human_iPSC_dox_neur_WT2


title: Foxp3EGFPCre Treg , 1

description: C


title: AIF3_M

description:
DESeq2_In_vivo_Liver_vs._Control_Liver.txt
DESeq2_In_vivo_Liver_vs._AOX_Liver.txt

value: Liver

value: In vivo developed


title: SCI_EtOH_12h_duplicate2

description: Gene Expression data

value: SCI

value: EtOH


title: Foxp3EGFPCre R26 N1c Cd22+ Treg, 3

description: B

value: Foxp3EGFPCre R26 N1c Cd22+ Treg


title: SCI_EtOH_6h_duplicate1

description: Gene Expression data


title: Foxp3EGFPCre R26 N1c Cd22+ Treg, 2

description: B


title: ACP3_M


title: libr57_human_iPSCdox_neur_WT1


title: libr81_human_iAstr_WT3


title: libr63_human_iFBN_WT4

source_name: forebrain-type cortical neurons (iFBN)

growth_protocol: iPS cells were differentiated in N3 media (50% DMEM/F12 with 0.5x GlutaMAX, 50% Neurobasal  with 1x Penicillin-Streptomycin, 0.5x B-27 minus vitamin A, 0.5x N2 supplement, 0.5x MEM Non-Essential Amino Acids (NEAA), 0.055 mM 2-mercaptoethanol and 1 µg/ml Insulin plus 1.5 µM Dorsomorphin and 10 µM SB431542. Media was replaced every day for 11 days. On day 12 Dorsomorphin and SB431542 were removed and cells continued to be fed each day with N3. N3 was supplemented with 0.05 µM Retinoic acid from days 16 through 20. Cells were split 1:2 with trypsin and replated onto Poly-L-ornithine, fibronectin  and laminin coated plates on day 20 into N4 media (same as N3 plus 0.05 µM Retinoic acid, 2 ng/ml BDNF and 2 ng/ml GDNF with Y-27632 dihydrochloride. Media was changed the following day to N4 media without Y-27632 dihydrochloride.

value: forebrain-type cortical neurons (iFBN)


title: ACP2_M

value: Male


title: Foxp3EGFPCre R26 N1c Cd22+ Treg, 1

description: B


title: SCI_EtOH_2h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, EtOH, 2h


title: ACP1_M


title: CTCF knockout biological replicate 6 RRBS

city: Los Angeles

first: Tom

last: Vondriska

state: CA

address: 650 Charles E Young Dr, BH553

institute: UCLA

library_source: genomic

data_processing:
Single-end reads were demultiplexed into sample-specific *.fastq files using custom scripts and then aligned to the mouse genome using the BSseeker2 v2.0.10.
Briefly, we built an mm10-based reference index—simply 40-400bp MspI restriction fragments digested in silico and consistent with our enriched fragment size—using the bs_seeker2-build.py script.
We then aligned single-end reads to the reference index with bs_seeker2-align.py, using the 40-400bp fragment size range and -r flag to indicate RRBS libraries, and allowing up to 5 mismatches. We selected Bowtie2 as the aligner within BSseeker2 for this step.
Samtools was used to sort the resulting .bam files, and methylation was called using bs_seeker2-call_methylation.py, using a 10 read coverage minimum for any given cytosine, and removing all reads that did not undergo full bisulfite conversion.
From the resulting CGmaps, we retained cytosines that exist within a CpG (cytosine followed by guanine) context. These are deposited herein as processed data.
Genome_build: mm10
Supplementary_files_format_and_content: CGmap files

molecule: genomic DNA

source_name: Isolated cardiac myocytes

extract_protocol:
DNA from left ventricular isolated adult cardiomyocytes was isolated using the QIAshredder kit (Qiagen).
Initial digestion into CpG rich regions was done by the Msp1 enzyme (NEB). The 3’ → 5’ Klenow exonuclease was used to repair sticky ends and promote poly-A tail synthesis. To facilitate multiplexing, individual TruSeq Illumina adapters were ligated to samples using the QIAseq Methyl Library Kit (Qiagen). Samples were then filtered to enrich for DNA fragments within the desired size range using magnetic AMPure XP beads (Beckman). Bisulfite conversion was performed using the Zymo EZ DNA Methylation-Lightning kit (Zymo).

treatment_protocol: DNA was isolated from mouse cardiomyocytes 3 days and 3 weeks after transverse aortic constriction (TAC) and CTCF depletion.

tag: genotype

value: CTCF knockout


title: MCL_LN_SOX11+ (99-08)

city: Barcelona

first: Virginia

last: Amador

email: VAMADOR@clinic.cat, PBALSAS@clinic.cat

state: Barcelona

address: Roselló 149-153

country: Spain

institute: IDIBAPS

hyb_protocol: Hybridization master mix was prepared and split into the 12 tubes containing the samples to analyze. Samples were then incubated in a PCR machine, for 16hours at 67ºC.

scan_protocol: cartridges were scanned and counted using the Nanostring scanner at its higher resolution (555 FOVs).

data_processing: Normalitzation with nSolver Analysis Software 4.0. Standard normalization uses a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within that sample lane.

source_name: Primary Mantle Cell Lymphoma (MCL)

label_protocol: Samples were labeled with Nanostring Reporter Probes.

extract_protocol: Nucleic acids were extracted from 10-µm sections of FFPE biopsies from lymph nodes using the QIAGEN AllPrep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) after deparaffinization according to the manufacturer´s instructions.

tag: sox11 status

value: Lymph node

value: Pretreated patient

tag: tumoral content


title: libr62_human_iFBN_WT3


title: ACP6_F

tag: strain

tag: developmental stage

value: Female


title: SCI_EtOH_0h_duplicate1

description: Gene Expression data

source_name: spinal cord  with injury, EtOH, 0h


title: SCI_EtOH_4h_duplicate1

description: Gene Expression data


title: ACF6_F

description:
DESeq2_In_vivo_Liver_vs._Control_Liver.txt
DESeq2_Control_Liver_vs._AOX_Liver.txt
DESeq2_In_Vitro_Control_Liver_vs._VIT_Control_Liver.txt

source_name: Murine 14.5 Liver


title: libr61_human_iFBN_WT2


title: CTCF knockout biological replicate 5 RRBS


title: SCI_EtOH_0h_duplicate2

description: Gene Expression data


title: libr60_human_iFBN_WT1


title: CTCF knockout biological replicate 4 RRBS


title: ACF4_F


title: TAC 3 days biological replicate 6 RRBS

value: TAC

value: 3 days


title: Lib42_CS25ID1C_MC


title: ACF3_M

value: In vitro control


title: Lib41_CS25ID1B_MC


title: ACF2_M


title: TAC 3 days biological replicate 4 RRBS


title: Lib40_CS25ID1A_MC


title: Lib39_CS25ID1C_XR


title: ACF1_M


title: TAC 3 weeks biological replicate 6 RRBS

value: 3 weeks


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 120h rep 2

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
Reads were aligned to the mouse GRCm38 primary assembly extended with the sequence of eGFP using STAR and the GENCODE annotation M5.
Low abundance reads were filtered out.
Genome_build: GRCm38
Supplementary_files_format_and_content: Filtered RPKM values

source_name: ER-Hoxa9-Lys-GFP cells

growth_protocol: Cell culturing in RPMI + 10% FBS + 1%SCF conditioned media + 1% pen/strp (+) or (-) E2

extract_protocol:
RNA was purified using an RNeasy mini kit
Library preparation was performed using an Illumina TruSeq RNA Library Prep Kit

treatment_protocol: (-) E2 treatment: 3X wash in PBS, change to media (-) E2

value: (-) E2 for 120 hours

value: cells culture in vitro


title: Lib38_CS25ID1B_XR


title: TAC 3 weeks biological replicate 5 RRBS


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 72h rep 2

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: Lib37_CS25ID1A_XR


title: ACF5_F

value: Liver

value: C57BL/6 x CBA F1


title: TAC 3 weeks biological replicate 4 RRBS


title: SCI_EtOH_2h_duplicate1

description: Gene Expression data

value: SCI

value: EtOH


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 40h rep 2

value: (-) E2 for 40 hours then +E2 add-back for 80 hours


title: Sham_MP_24h_duplicate1

description: Gene Expression data

source_name: spinal cord  without injury, MP, 24h

value: Sham

value: MP


title: Sham_MP_48h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, MP, 48h


title: Control biological replicate 5 RRBS

value: Control


title: TAC 3 days biological replicate 5 RRBS


title: Sham_MP_24h_duplicate2

description: Gene Expression data


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 24h rep 2

value: (-) E2 for 24 hours then +E2 add-back for 96 hours


title: Sham_MP_12h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, MP, 12h


title: Sham_MP_12h_duplicate1

description: Gene Expression data


title: Sham_MP_48h_duplicate1

description: Gene Expression data


title: Sham_MP_8h_duplicate1

description: Gene Expression data

source_name: spinal cord  without injury, MP, 8h


title: Control biological replicate 4 RRBS


title: Lib35_33ID2V2B_MC

value: forebrain-type cortical neurons (iFBN)


title: Sham_MP_6h_duplicate1

description: Gene Expression data

source_name: spinal cord  without injury, MP, 6h


title: Sham_MP_8h_duplicate2

description: Gene Expression data


title: Sham_MP_6h_duplicate2

description: Gene Expression data


title: Lib34_33ID2V2A_MC


title: RNA-seq ER-Hoxa9-Lys-GFP (+) E2 (untreated) rep 2

value: (+) E2 (untreated)


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 120h Rep 1


title: Control biological replicate 3 RRBS


title: Lib33_33ID2V1C_MC


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 72h Rep 1


title: Lib32_33ID2V1B_MC


title: N3

city: Manhattan

first: Aliza

last: Rubenstein

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description: Genomic and Viral RNA

data_processing:
Cell Ranger 3.1.0 used for data demultiplexing and alignment to the Mesocricetus auratus and SARS-CoV-2 genomes.
STAR 2.7.0 in STARsolo mode used for alignment to the SARS-CoV-2 genome with the addition of 3' and 5' ends of the genome as genes.
Genome_build: MesAur1.0+ASM985889v3
Supplementary_files_format_and_content: h5 matrices (hamster reads) and 10X output sparse matrices in folder format (viral reads)

organism: Mesocricetus auratus

source_name: Lung Cells

extract_protocol:
The cranial left lung sections taken at the time of necropsy at 4 dpi from the 5 µg prime-boost group (VI, n=5), mock vaccinated group (MI, n=5) and a naïve group (N, n=4) of hamsters that were mock infected via the IN route with 100 µL of media inoculum. Lung samples were enzymatically digested and homogenized using the Lung Dissociation kit, mouse (Miltenyi Biotec Cat No. 130-095-927) and GentleMACS Dissociator (Miltenyi Biotec) according to the manufacturers protocol. After 30 min of digestion, the samples were filtered through a 70 µM filter, and RBC lysis was performed (ThermoFisher, MA, Cat #00-4333-57). After two washes in PBS containing 0.05 mM EDTA, the cell pellet was re-suspended in 1ml of buffer and filtered through a 40 µM Flowmi Cell strainer (Bel-Art # H13680-0040). The cell viability and concentration were determined on a TC20 cell counter (Bio-Rad, CA). Dead cell removal was performed if the viability was lower than 80% using Dead Cell Removal Kit (Miltenyi Biotec, CA, Cat#130-090-101) as per manufacturers recommendations.
Seven thousand cells were targeted for generation of barcoded gel bead emulsions using the Chromium Single Cell 3’ version 3.0 chemistry (10x Genomics, CA, Cat# 1000077). After reverse transcription, the cDNA was amplified and purified using SPRISelect magnetic beads (Beckman Coulter, CA, Cat#B23317). The purified cDNA was precipitated in 80% ethanol, removed from BSL-4 containment, tested for quality on Bioanalyzer, and 3’ gene expression libraries were prepared as per manufacturer’s instructions. Libraries were quantified, and pooled libraries were submitted for sequencing (~140,000 reads per sample) on Novaseq S1 Flow cell (New York Genome Center).

value: FALSE


title: Lib36_33iD2V2C_MC


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 40h Rep 1


title: Sham_MP_4h_duplicate1

description: Gene Expression data

source_name: spinal cord  without injury, MP, 4h

treatment_protocol: Following different time after MP, EPO or control medication, SCI animals were anesthetized with a mixture of Zoletil 50 and Rompun described earlier and the 5-mm lesion spinal cord was removed, frozen immediately in liquid nitrogen and stored in liquid nitrogen prior to RNA extraction. Total RNA was extracted by the Trizol method and the integrity of RNA was examined by Agilent Bioanalyzer (Agilent Technologies, Inc. Headquarters, Palo Alto, CA, USA) before oligo microarray analysis started.


title: Sham_MP_4h_duplicate2

description: Gene Expression data


title: N4

description: Genomic and Viral RNA


title: Lib31_33ID2V1A_MC


title: Sham_MP_2h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, MP, 2h


title: RNA-seq ER-Hoxa9-Lys-GFP (-) E2 24h Rep 1


title: N2

description: Genomic and Viral RNA


title: N1

description: Genomic and Viral RNA


title: ovary, metastasis from lobular breast cancer, region 2

type: genomic

city: Hannover

first: Helge

last: Stark

address: Carl-Neuberg-Straße 1

department: Institute of Pathology

country: Germany

institute: Medical School Hannover

description: internal ID D46

hyb_protocol: EZ-96 DNA Methylation-Lightning Kit and according to Infinium HD AssayMethylation Protocol

scan_protocol: According to Infinium HD AssayMethylation Protocol

data_processing:
R packages: MethylAid (version 1.12.0), ChAMP (version 2.9.10)
the non_normalized.txt contains unmethylated and methylated signal intensities

label: QuDye dsDNA

label_protocol: Qubit dsDNA HS assay kit (Life Technologies, Carlsbad, U.S.A.)

extract_protocol: Maxwell RSC DNA FFPE Kit (Promega, Madison, U.S.A.) on a Maxwell RSC instrument (Promega)

tag: gender

value: female

value: ovary

tag: region type

value: glandular


title: RNA-seq ER-Hoxa9-Lys-GFP (+) E2 (untreated) Rep 1

tag: treatment

value: cells culture in vitro


title: ER-Hoxa9-Lys-GFP (-) E2 120 hours Rep 2

data_processing:
Raw data were mapped to mouse reference genome version mm9 by BWA and potential PCR duplicates and ambiguously mapped reads were filtered out.
Peaks were called by MACS 2.0 with parameters callpeak --nomodel --extsize 200 --shift -100 -q 0.01
Paired-end clean reads were aligned to the reference genome using STAR (v2.5), using the Maximal Mappable Prefix (MMP) method.
Consistency of peak calling results between replicates was examined using IDR analysis. IDR consistency threshold of 0.05 was applied to truncate the peak lists, peaks that passed the threshold were used for subsequent analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Peak coordinate BED files (Rep 1 and Rep 2 samples merged for a given timepoint)

extract_protocol:
Nuclei isolated from 100,000 cells using 100 ul hypotonic lysis buffer to generate two independent transposition reactions. Nuclei were split in half and treated with 2.5 ul Tn5 Transposase (Illumina) for 30 mins at 37 degrees celsius.
DNA from transposed nuclei was isolated and PCR-amplified using barcoded Nexteral primers (Illumina). Library QC was carried out using a high sensitivity DNA bioanalyzer assay and quibit measurement.


title: ER-Hoxa9-Lys-GFP (-) E2 96 hours Rep 2

value: (-) E2 96 hours


title: Lib27_33ID2V1C_XR


title: Sham_MP_2h_duplicate1

description: Gene Expression data


title: Lib28_33ID2V2A_XR


title: MI4

description: Genomic and Viral RNA

value: TRUE


title: Mi2

description: Genomic and Viral RNA


title: MI3

description: Genomic and Viral RNA


title: ER-Hoxa9-Lys-GFP (-) E2 72 hours Rep 2

value: (-) E2 72 hours


title: ER-Hoxa9-Lys-GFP (-) E2 36 hours Rep 2

value: (-) E2 36 hours


title: MI5

description: Genomic and Viral RNA


title: Sham_EtOH_48h_duplicate1

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 48h

value: EtOH


title: Lib26_33ID2V1B_XR


title: Sham_EtOH_24h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 24h


title: Lib24_33ID1V2C_MC

source_name: forebrain-type cortical neurons (iFBN)


title: Lib25_33ID2V1A_XR


title: ER-Hoxa9-Lys-GFP (-) E2 48 hours Rep 2

value: (-) E2 48 hours


title: ER-Hoxa9-Lys-GFP (-) E2 24 hours Rep 2

value: (-) E2 24 hours


title: Sham_EtOH_12h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 12h

value: Sham


title: Lib30_33ID2V2C_XR


title: Sham_EtOH_24h_duplicate1

description: Gene Expression data


title: Sham_EtOH_48h_duplicate2

description: Gene Expression data


title: VI5

description: Genomic and Viral RNA

value: Vaccinated


title: Lib22_33iD1V2A_MC


title: VI4

description: Genomic and Viral RNA


title: Sham_EtOH_8h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 8h


title: Sham_EtOH_12h_duplicate1

description: Gene Expression data


title: Lib23_33ID1V2B_MC


title: Lib29_33iD2V2B_XR


title: MI1

description: Genomic and Viral RNA


title: VI3

description: Genomic and Viral RNA


title: ER-Hoxa9-Lys-GFP (-) E2 8 hours Rep 2

value: (-) E2 8 hours


title: VI2

description: Genomic and Viral RNA


title: Sham_EtOH_6h_duplicate1

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 6h


title: Sham_EtOH_8h_duplicate1

description: Gene Expression data


title: Lib19_33ID1V1A_MC

value: forebrain-type cortical neurons (iFBN)


title: VI1

description: Genomic and Viral RNA


title: Sham_EtOH_6h_duplicate2

description: Gene Expression data


title: ER-Hoxa9-Lys-GFP (-) E2 12 hours Rep 2

value: (-) E2 12 hours


title: ER-Hoxa9-Lys-GFP (-) E2 120 hours Rep 1


title: Lib18_33ID1V2C_XR


title: ER-Hoxa9-Lys-GFP (-) E2 96 hours Rep 1


title: ER-Hoxa9-Lys-GFP (-) E2 72 hours Rep 1


title: Lib16_33ID1V2A_XR


title: Sham_EtOH_4h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 4h


title: Sham_EtOH_2h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 2h


title: Lib21_33ID1V1C_MC


title: ER-Hoxa9-Lys-GFP (-) E2 48 hours Rep 1

source_name: ER-Hoxa9-Lys-GFP cells


title: shDrp1-LCL768

city: Charleston

first: Natalia

last: Oleinik

state: SC

address: 87 Jonathan Lucas St

department: Biochemistry

institute: MUSC

hyb_protocol: followed the manufacturer's instructions: NanoString Technologies (Seatlle, WA)

data_processing: number of reads was normalized by housekeeping genes in the panel using nCounter nSolver Software

label: NanoString

source_name: UM-SCC-1A, H&N cancer cells

label_protocol: the extract was not labeled

growth_protocol: cells were grown in DMEM, media supplemmented with NAAA, a/b and 10%FBS; 5.0% CO2, 37C; media were changed and cells were splitted every 2-3 days;

extract_protocol: total RNA was extracted from 100.000 cells using RNA easy extraction Mini kit (Qiagen)

treatment_protocol: on the day before the experiment cells were seeded in 6-well plates at the density of 300.000 cells/well; next day they were treated either with PBS/ 10 µM of Sodium Selenite (SoSe) or Et/OH or 10 µM for 3h

tag: cell line

tag: cell type

value: Head and neck cancer cells

value: stable Drp1shRNA cells treated with LCl768 for 3 h


title: Scr-LCL768

scan_protocol: followed the manufacturer's instructions: NanoString Technologies (Seatlle, WA)

value: stable ScrshRNA cells treated with LCl768  for 3 h


title: Lib17_33ID1V2B_XR


title: Lib15_33iD1V1C_XR


title: ER-Hoxa9-Lys-GFP (-) E2 4 hours Rep 2

value: (-) E2 4 hours

tag: tissue


title: shP17-Rbmut-V.2

value: stable P17shRNA cells,ectopically expressing P17RbMut protein and  treated with PBS (V2) for 3 h


title: ER-Hoxa9-Lys-GFP +E2 (untreated) Rep 2

value: untreated (+E2)

value: cells culture in vitro


title: Sham_EtOH_4h_duplicate1

description: Gene Expression data


title: ER-Hoxa9-Lys-GFP (-) E2 36 hours Rep 1


title: shDrp1-V.1

value: stable Drp1shRNA cells treated with ET/PBS (V1) for 3 h


title: Sham_EtOH_0h_duplicate2

description: Gene Expression data

source_name: spinal cord  without injury, EtOH, 0h


title: Sham_EtOH_2h_duplicate1

description: Gene Expression data


title: ER-Hoxa9-Lys-GFP (-) E2 24 hours Rep 1


title: Lib13_33ID1V1A_XR


title: Lib14_33ID1V1B_XR


title: Sham_EtOH_0h_duplicate1

description: Gene Expression data


title: Lib20_33ID1V1B_MC


title: ER-Hoxa9-Lys-GFP (-) E2 12 hours Rep 1


title: Scr-V1.

value: stable ScrshRNA cells treated with Et/PBS (V1) for 3 h


title: Lib48_HT223_B_C_XR

source_name: iPSC

growth_protocol: iPSCs were grown on matrigel hESC qualified matrix (Corning) coated plates in mTeSR1 (Stemcell Technologies)

value: iPSC


title: ER-Hoxa9-Lys-GFP (-) E2 8 hours Rep 1


title: shP17.WTP17-SoSe

value: stable P17shRNA cells,ectopically expressing P17WT protein and  treated with SoSe for 3 h


title: Lib47_HT223_B_B_XR


title: ER-Hoxa9-Lys-GFP +E2 (untreated)  Rep 1


title: shP17-Rbmut-SoSe

value: stable P17shRNA cells,ectopically expressing P17RbMut protein and  treated with SoSe  for 3 h


title: shP17-SoSe

value: stable P17shRNA cells treated with SoSe for 3 h


title: Lib46_HT223_B_A_XR


title: Scr-SoSe

value: stable ScrshRNA cells treated with SoSe for 3 h


title: Lib45_A18945_C_XR


title: ER-Hoxa9-Lys-GFP (-) E2 120h Input

data_processing:
Reads aligned to genome using Bowtie 2.0 (for histone modification ChIP-seq) or BWA with default settings (for V5-Hoxa9-AM/V5-ER-Hoxa9-AM ChIPs)
Duplicate reads removed
Peaks called with MACS 2.0, with NarrowPeak setting used for H3K27ac ChIP-seq and BroadPeak setting used for H3K27me3 ChIP-seq
Genome_build: mm9 (H3K27ac and H3K27me3 ChIP-seq) and mm10 (H3K4me3, V5-Hoxa9-AM, and V5-ER-Hoxa9-AM ChIP-seq)
Supplementary_files_format_and_content: Peak coordinate bed files

extract_protocol:
Formaldehyde fixation, nuclear isolation, probe sonication, ChIP of 500 ug chromatin (for histone modification ChIPs) or 30 ug chromatin (for V5-Hoxa9-AM/V5-ER-Hoxa9-AM ChIPs) with 4-10 ug antibody, cross-link reverasal, proteinase K treatment, and DNA purification via phenol chloroform extraction.
NEBNext ChIP-seq Library Master Mix Set for Illumina kit with AMPure XP beads for purification.

value: (-) E2 for 120 hours

value: cells cultured in vitro

tag: antibody


title: Lib44_A18945_B_XR


title: ACX at T72, biological rep2

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

institute: Universidad de Malaga

description: Gene expression data from leaves of similar size and development stages of Arabidopsis thaliana

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Expression data were normalized using the Robust Multi-array Average (RMA) algorithm implemented in the aﬀyPLM package. Differential gene expression was based on linear models for analysing microarray data (LIMMA). Differentially expressed (DE) genes were obtained by paired comparisons, with two independent comparisons carried out for each combination of treated samples vs. control for each genotype. Only genes with a fold-change (FC) over 1.5 (|log2(FC)| > 0.58496) and an adjusted P < 0.05 (adjusted using the false discovery rate (FDR) method developed by Benjamini‐Hochberg) were considered for further investigation.

organism: Arabidopsis thaliana

source_name: Leaves of similar sizes and developmental stages of Arabidopsis ACX at 72h treatment.

label_protocol: standard Affymetrix protocol

growth_protocol: Seeds were sown in moistened soil and grown in 16 h light and 8 h dark photoperiod cycles at 22 and 20 ºC, respectively, under 120 µE and at 60 % relative humidity

extract_protocol: Isolated total RNA was treated with deoxyribonuclease I (DNaseI; Turbo DNA free, Thermo Fisher Scientific) and cleaned on RNeasy Mini columns (Qiagen).

treatment_protocol: The effect of 2,4-dichlorophenoxyacetic acid (2,4-D) on Arabidopsis plants was analysed by spraying 23 mM 2,4-D solution (1% dimethyl sulfoxide acid, DMSO and 1% EtOH), and plant leaves were collected after 1 and 72 h post treatment (hpt). Control plants were sprayed with 1% DMSO and 1% EtOH. Treatment times, 2,4-D concentrations and treatment techniques used in this study had been previously optimised

value: Leaves

value: ACX

tag: age


title: ACX at T72, biological rep1

value: Leaves of similar sizes and developmental stages of Arabidopsis


title: shP17.WTP17-V2

value: Head and neck cancer cells

value: stable P17shRNA cells,ectopically expressing P17WT protein and  treated with PBS (V2) for 3 h


title: ER-Hoxa9-Lys-GFP (-) E2 72h Input

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: GFI1KO_G2ECs_2

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: GATA2+_ECs derived in GFI1KO

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: Endothelial cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESCs derived Endothelial cells


title: ACX at T72, biological rep3


title: ER-Hoxa9-Lys-GFP (-) E2 56h Input

value: (-) E2 for 56 hours then +E2 add-back for 64 hours


title: Scr-V2

value: stable ScrshRNA cells treated with PBS (V2) for 3 h


title: Lib43_A18945_A_XR


title: ACX at T1, biological rep2

source_name: Leaves of similar sizes and developmental stages of Arabidopsis ACX at 1h treatment.


title: Lib12_CS25IC_MC


title: ER-Hoxa9-Lys-GFP (-) E2 4 hours Rep 1

value: (-) E2 4 hours

value: cells culture in vitro


title: ER-Hoxa9-Lys-GFP (-) E2 40h Input

value: (-) E2 for 40 hours then +E2 add-back for 80 hours


title: ACX at T1, biological rep1


title: ACX at T0, biological rep5

source_name: Leaves of similar sizes and developmental stages of Arabidopsis ACX at 0h treatment


title: ACX at T0, biological rep6


title: ACX at T1, biological rep3


title: Lib11_CS25IB_MC

value: iPSC


title: shP17-V2

value: stable P17shRNA cells treated with PBS (V2) for 3 h


title: Lib10_CS25IA_MC


title: ER-Hoxa9-Lys-GFP (-) E2 24h Input

value: (-) E2 for 24 hours then +E2 add-back for 96 hours


title: WT_G2ECs_1

description: GATA2+_ECs derived in WT

value: WT


title: ACX at T0, biological rep3


title: ER-Hoxa9-Lys-GFP (+) E2 (untreated) Input

value: (+) E2 (untreated)

value: cells cultured in vitro


title: ACX at T0, biological rep2

value: Leaves

value: ACX


title: Lib6_CS25IC_XR


title: GFI1KO_G2ECs_1

description: GATA2+_ECs derived in GFI1KO


title: Lib5_CS25IB_XR


title: ER-Hoxa9-Lys-GFP (-) E2 120h H3K27me3 ChIP

value: (-) E2 for 120 hours


title: ER-Hoxa9-Lys-GFP (-) E2 72h H3K27me3 ChIP


title: ACX at T0, biological rep4

value: Leaves of similar sizes and developmental stages of Arabidopsis


title: Lib4_CS25IA_XR


title: RPE 2

city: Chongqing

first: Zongren

last: Xu

state: Chongqing

address: 1 Youyi Road, Yuzhong District, Chongqing, China

department: ophthalmology department

institute: The First Affiliated Hospital of Chongqing Medical University

description: one sample from human eye tissue

data_processing:
Single cells were assessed using a 10× Chromium system (10× Genomics) and V2 single-cell reagent kits. After the library was built, the reads were aligned to the GRch38 human genome using the 10× analysis tool Cellranger Toolkit (Version 2.1.1), and a unique molecular identifier (UMI) was used to quantify gene expression. Cellranger Count was used to preprocess and preliminarily filter the data. Generate three files matrix.mtx,genes.tsv and barcodes.tsv.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Eye

extract_protocol:
The RPE tissues were rinsed three times with phosphate-buffered saline (PBS). First, the tissues were digested using 0.25% trypsin for approximately 30 min at 37°C until a single-cell suspension was made, and then complete Dulbecco's Modified Eagle Mediummodified Eagle’s medium (DMEM) was used to neutralize the cell suspension. The single-cell samples were passed through a 40 μm cell strainer. Second, the cell suspension was rinsed three times with PBS and centrifuged for 5 min (1,450 rpm, 4°C). Next, a hemocytometer with trypan blue was used to count the number of cells and ensure that the level of cell viability was approximately 90%. Finally, single-cell samples were subjected to scRNA-seq analysis with a high-throughput droplet-mediated scRNA-seq platform (10× Genomics Chromium).
The appropriate volume of each sample was diluted to contain approximately 5,000 hRPE cells. Subsequently, the single-cell suspension, gel beads and oils were all added to the 10× Genomics single-cell A chip. After droplet generation, samples were transferred into 200 μl PCR tubes, and reverse transcription was performed using a T100 Thermal Cycler (Bio-Rad, California, USA). After reverse transcription, cDNA was recovered using a recovery agent provided by 10× Genomics. SPRIselect beads were used for cDNA clean-up, and then the cDNA was amplified for 10 cycles. The concentration of cDNA was detected by a Qubit2.0 fluorometer (Invitrogen, Canada). Single-cell cDNA libraries were prepared according to the Chromium Single Cell 3’ Reagent Kit v2 user guidance (https://support.10xgenomics.com/single-cell-gene-expression/index/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry).

value: retinal pigment epithelium

value: adult


title: RPE 3

description: one sample from human eye tissue


title: ACX at T0, biological rep1


title: ER-Hoxa9-Lys-GFP (-) E2 40h H3K27me3 ChIP


title: RPE 1

description: one sample from human eye tissue


title: WT at T72, biological rep3

source_name: Leaves of similar sizes and developmental stages of Arabidopsis WT   at 72 h treatement


title: ER-Hoxa9-Lys-GFP (-) E2 24h H3K27me3 ChIP


title: WT at T72, biological rep2


title: Lib9_33IC_MC


title: 502-063

city: Newton

first: Christopher

last: Walker

address: 85 Wells Ave

institute: Karyopharm Therapeutics, Inc

description: ribodepleted RNA

data_processing:
RNAseq reads were aligned with HiSAT2.
Gene-level expressions were determined with featurecounts.
Gene expression normalization and comparison were performed with DESeq2.
RNAseq data were used to infer the activities of 6,203 regulatory proteins, including proteins annotated as Transcription Factors (GO:0003700, or GO:0004677 and GO:0030528 or GO:0045449), co-Transcription Factors (GO:0003712 or GO:0030528 or GO:0045449), and signaling proteins (GO:0007165 and GO:0005622 or GO:0005886) in Gene Ontology. Protein activity was measured by Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER), which converts tumor sample gene-expression profiles into accurate protein activity profiles, using a GBM context-specific model of transcriptional regulation (interactome) available from Bioconductor (https://www.bioconductor.org/packages/release/data/experiment/html/aracne.networks.html).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gbm_rawcounts.tsv: Raw counts for each gene in each Sample.
Supplementary_files_format_and_content: gbm_vpmat.tsv: Protein activities.

source_name: glioblastoma tumor

extract_protocol: TruSeq™ Stranded Total RNA With Ribo-Zero™ Plus rRNA Depletion protocol (Illumina).

treatment_protocol:
NCT01986348
Experimental: Arm A: Selinexor 60 mg and Surgery
Participants who required surgery received up to 3 doses of oral selinexor tablets 60 milligrams (mg) twice weekly (BIW) on Day 1, Day 3 and between 2 and 48 hours prior to surgery, subsequently underwent surgery for resection of their tumor and resumed selinexor tablets 60 mg BIW after recovery, during Week 1 to 4 of each 4-week cycle, until progression of disease (PD) or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330
Experimental: Arm B: Selinexor 50 mg/m^2
Participants who were not eligible for surgery received selinexor tablets 50 mg per square meter (mg/m^2) BIW during Week 1 to 4 of each 4-week cycle until PD or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330
Experimental: Arm C: Selinexor 60 mg
Participants who were not eligible for surgery received selinexor tablets 60 mg BIW during Week 1 to 4 of each 4-week cycle until PD or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330
Experimental: Arm D: Selinexor 80 mg
Participants who were not eligible for surgery received selinexor tablets 80 mg once weekly (QW) during Week 1 to 4 of each 4-week cycle until PD or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330

value: glioblastoma tumor

tag: trial arm

value: C

tag: experimental set

value: Discovery

tag: patient response

value: Non-responder


title: WT_G2ECs_2

description: GATA2+_ECs derived in WT

value: hESCs derived Endothelial cells


title: Lib8_33iB_MC

tag: donor line

tag: tissue/cell type

value: iPSC


title: 502-062

description: ribodepleted RNA

value: D

value: Responder


title: ER-Hoxa9-Lys-GFP (+) E2 (untreated) H3K27me3 ChIP


title: Lib7_33IA_MC


title: Lib3_33IC_XR


title: 502-052

description: ribodepleted RNA

value: Validation


title: ER-Hoxa9-Lys-GFP (-) E2 120h H3K27ac ChIP


title: Lib2_33IB_XR


title: ER-Hoxa9-Lys-GFP (-) E2 56h H3K27ac ChIP

value: (-) E2 for 56 hours then +E2 add-back for 64 hours


title: 501-061

description: ribodepleted RNA


title: 501-059

description: ribodepleted RNA


title: ER-Hoxa9-Lys-GFP (-) E2 40h H3K27ac ChIP

value: (-) E2 for 40 hours then +E2 add-back for 80 hours

value: cells cultured in vitro


title: ER-Hoxa9-Lys-GFP (-) E2 72h H3K27ac ChIP

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: 501-058

description: ribodepleted RNA


title: 501-056

description: ribodepleted RNA

value: Excluded Outlier


title: Lib1_33iA_XR


title: ER-Hoxa9-Lys-GFP (-) E2 120h H3K4me3 ChIP

value: (-) E2 for 120 hours


title: WT at T72, biological rep1

source_name: Leaves of similar sizes and developmental stages of Arabidopsis WT  at 72 h treatement

value: Leaves

tag: genotype

value: WT


title: TL1 cell line

city: Rotterdam

first: Anton

middle: W

last: Langerak

state: Zuid Holland

address: Dr. Molewaterplein 40

department: Immunology

country: Netherlands

institute: ErasmusMC

description: Small non-coding RNA sequencing out of cells from a T-LGL cell line model

data_processing:
After sequencing and de-multiplexing the quality of the data was assessed with fastQC (v 0.11.8).
When the RNA sequence data passed the quality check, fastq files were aligned using STAR aligner (v.2.5.3e) with GRCh38 as reference.
The small non-coding RNA reads were trimmed and aligned with Novalign, using novoalign indexes.
Read counts were obtained using FeatureCounts (v1.6.0) and Homo_sapiens GRCh38.92 as reference and miRBase.annotation20 for miRNA sequence data.
The quality of the alignment and assigned reads were determined with MultiQC.Noise reduction was applied to the count data by removing the very low read counts.
Normalized data was used for visualization and comparison purposes, which include correlation and clustering analysis generating the heatmaps and PCA plots.
For the differential expression analysis, DESeq2 (R package v1.22.2) was used.
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv and .counts files containing raw RNA counts per gene

source_name: cells from a T-LGL cell line model

growth_protocol: Patient or healthy control PBMCs were thawed and added to 1 ml of ice-cold FCS before adding 8 ml of pre-warmed Roswell Park Memorial Institute (RPMI) 1640 Medium, GlutaMAX™ Supplement, HEPES (Sigma Aldrich, Saint Louis, MA, USA) supplemented with 10% bovine serum albumin (BSA) and 1% penicillin and streptomycin. Cells were stained and sorted based on aberrant expression levels of CD2, CD5, and/or CD7 and/or high expression of CD57. Age-matched healthy control PBMCs were stained and terminally differentiated effector memory cells (CD3+/CD8+/TCRγδ-/CD45RA+/CCR7-; TEMRA) were sorted as control populations. All sorting experiments were performed using the FACS Aria III instrument. Use of T-LGL samples was approved by the Erasmus MC Institutional Review Board (MEC2015-617). Control samples were obtained from Sanquin Blood Bank (Amsterdam, The Netherlands). All healthy blood donors were included upon informed consent and anonymized prior to use (MEC2016-202)

extract_protocol:
T-LGL and healthy control CD8 TEMRA cells were lysed in Trizol (Invitrogen) and total RNA was isolated according to manufacturer’s protocol. Quality and concentration of total RNA of the samples was determined with the RNA 6000 Nano assay on an Aligent 2100 Bioanalyzer (Agilent Technologies).
The small non-coding RNA cDNA libraries were generated with 1 ng total RNA using CleanTag Small RNA Library Preparation Kit (Trilink Biotechnologies) according to the manufacturer’s protocol.

value: TL1 (a human T-LGL cell line model)

value: CD8+ T cells

tag: sorted cells

value: TL1 cells

tag: disease state

value: leukemia


title: LGL148

description: Small non-coding RNA sequencing out of sorted T-LGL cells from PBMCs from patients with T-LGL leukemia

value: Peripheral Blood Mononuclear Cells

value: T-LGL cells


title: LGL052

source_name: sorted T-LGL cells from PBMCs from patients with T-LGL leukemia


title: ER-Hoxa9-Lys-GFP (-) E2 24h H3K27ac ChIP

tag: strain

value: (-) E2 for 24 hours then +E2 add-back for 96 hours


title: 501-054

description: ribodepleted RNA

value: glioblastoma tumor

value: C

value: Responder


title: ER-Hoxa9-Lys-GFP (+) E2 (untreated) H3K27ac ChIP

value: (+) E2 (untreated)


title: WT at T1, biological rep3

source_name: Leaves of similar sizes and developmental stages of Arabidopsis WT  at 1 h treatement


title: mouse_Sham+Saline_3

city: Brisbane

first: Jean-Pierre

last: Levesque

state: Queensland

address: 37 Kent St

department: Mater Research Institute

institute: Mater Research Institute-University of Queensland

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips and read on a BeadStation 500 System using Beadscan software Version 3.5.31 (Illumina)

data_processing: Microarray data were analyzed by Illumina Genomestudio software (v2011.1), Gene Expression module (V1.9.0) average normalization algorithms with background subtraction followed by Illumina custom differential analysis algorithms.

source_name: muscle

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Whole hindlinb muscle were sampled 2 days post-surgery and homogenized in 4 ml of Trizol (Invitrogen) with TissueRuptorII (Qiagen Hilden) or IKA T10 basic homogenizer on ice for 30 seconds for 3 times with 10 second intervals followed by incubation at RT for 30 minutes. Tissue debris were removed by centrifuging at 12,000xg and supernatants were mixed with 1/5 volume of chloroform. After spinning down at 12,000xg, 4°C for 15 mins, aqueous phases containing RNA were transferred to fresh tubes for RNA precipitation with isopropanol. The RNA pellets were further washed in 75% ethanol, air-dried and dissolved in RNAse/DNase free water.

treatment_protocol: Mice were divided in 4 groups that underwent the following surgeries 1) SCI between vertebrae T12-13+ intramuscular CDTX; 2) SCI+ intramuscular Saline; 3) Sham surgery + intramuscular CDTX; 4) Shamsurgery + Intramuscular saline.

value: Sham+Saline

tag: time

value: 2 days post surgery

tag: gender

value: Female

value: muscle


title: WT at T1, biological rep2

value: Leaves

value: Leaves of similar sizes and developmental stages of Arabidopsis


title: 501-049

description: ribodepleted RNA

value: Validation


title: LGL141


title: WT at T0, biological rep6

source_name: Leaves of similar sizes and developmental stages of Arabidopsis WT at 0 h treatement

value: WT


title: WT at T1, biological rep1

source_name: Leaves of similar sizes and developmental stages of Arabidopsis WT at 1 h treatement


title: mouse_Sham+Saline_4

tag: treatment


title: WT at T0, biological rep4


title: ER-Hoxa9-Lys-GFP (-) E2 40h H3K4me3 ChIP

source_name: ER-Hoxa9-Lys-GFP cells

value: (-) E2 for 40 hours then +E2 add-back for 80 hours

value: cells cultured in vitro


title: WT at T0, biological rep5


title: WT at T0, biological rep2


title: WT at T0, biological rep1


title: WT at T0, biological rep3


title: LGL028

value: Peripheral Blood Mononuclear Cells

value: leukemia


title: LGL018

value: T-LGL cells


title: LGL030


title: ER-Hoxa9-Lys-GFP (-) E2 72h H3K4me3 ChIP

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: mouse_Sham+Saline_2


title: 501-053

description: ribodepleted RNA

value: glioblastoma tumor

value: D

value: Discovery

value: Non-responder


title: ER-Hoxa9-Lys-GFP (-) E2 24h H3K4me3 ChIP

value: (-) E2 for 24 hours then +E2 add-back for 96 hours


title: 301-044

description: ribodepleted RNA

value: C


title: mouse_Sham+Saline_1

value: Sham+Saline

value: 2 days post surgery

value: Female

value: muscle


title: ER-Hoxa9-Lys-GFP (+) E2 (untreated) H3K4me3 ChIP

value: (+) E2 (untreated)


title: mouse_Sham+CDTX_3

value: Sham+CDTX


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 120h rep 2

value: (-) E2 for 120 hours

value: cells culture in vitro


title: 501-048

description: ribodepleted RNA

value: Excluded Outlier


title: LGL002

value: Peripheral Blood Mononuclear Cells

value: T-LGL cells

value: leukemia


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 56h rep 2

value: (-) E2 for 56 hours then +E2 add-back for 64 hours


title: CD8EF_22_6

description: Small non-coding RNA sequencing out of sorted CD8 TEMRA cells from healthy donor PBMCs

value: no leukemia


title: mouse_Sham+CDTX_2


title: mouse_Sham+CDTX_1


title: 301-033

description: ribodepleted RNA

value: glioblastoma tumor

value: D

value: Non-responder


title: CD8EF_28_6

source_name: sorted CD8 TEMRA cells from healthy donor PBMCs


title: 301-028

description: ribodepleted RNA


title: mouse_Sham+CDTX_4


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 72h rep 2

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 40h rep 2

value: (-) E2 for 40 hours then +E2 add-back for 80 hours


title: mouse_SCI+saline_4

value: SCI+saline

value: 2 days post surgery

value: Female


title: 301-025

description: ribodepleted RNA

value: B

value: Validation


title: CD8_Effector_22_6


title: 301-045

description: ribodepleted RNA

value: C

value: Discovery


title: CD8_Effector_28_6

value: Peripheral Blood Mononuclear Cells


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 24h rep 2

value: (-) E2 for 24 hours then +E2 add-back for 96 hours

value: cells culture in vitro


title: 301-022

description: ribodepleted RNA


title: 301-013

description: ribodepleted RNA

value: Responder


title: CD8_Effector_15_6

value: no leukemia


title: mouse_SCI+saline_2

value: muscle


title: ATAC-seq ER-Hoxa9-Lys-GFP (+) E2 (untreated) rep 2

value: (+) E2 (untreated)


title: RA_HC_2

city: Seoul

first: Eun Bong

last: Lee

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University College of Medicine

data_processing:
The sequence reads were analyzed by alignment to the Human Ensembl Archive Release 90 using STAR with ENCODE options and quantification using RSEM.
Differentially expressed genes were identified by DESeq2 with Wald test and Likelihood ratio test corrected by Benjamini-Hochberg procedure (FDR<0.05) and one-way ANOVA (P<0.01) corrected by FDR<0.05.

source_name: FACS-sorted Tscm cells

extract_protocol: Total RNA was isolated from FACS-sorted Tscm cells (derived from PBMC) using RNeasy mini kit or RNeasy Plus Micro kit (Qiagen). RNA-seq libraries were produced using the NEXTflex Rapid Directional mRNA-Seq Kit Bundles (Bioo scientific) and sequenced on the Illumina HiSeq 2500 platform.

tag: cell

value: PBMC

value: healthy control


title: mouse_SCI+saline_3


title: 301-005

description: ribodepleted RNA

value: glioblastoma tumor


title: 301-039

description: ribodepleted RNA


title: mouse_SCI+saline_1

value: SCI+saline


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 120h Rep 1

value: (-) E2 for 120 hours


title: RA_HC_1


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 72h Rep 1

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: 301-004

description: ribodepleted RNA

value: B

value: Non-responder


title: mouse_SCI+CDTX_4

value: SCI+CDTX

value: 2 days post surgery

value: Female


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 56h Rep 1

value: (-) E2 for 56 hours then +E2 add-back for 64 hours


title: mouse_SCI+CDTX_3


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 40h Rep 1

value: (-) E2 for 40 hours then +E2 add-back for 80 hours

value: cells culture in vitro


title: 301-002

description: ribodepleted RNA

value: A

value: Excluded Outlier


title: 301-003

description: ribodepleted RNA

value: Discovery


title: RA_remission_1

value: PBMC

value: rheumatoid arthritis in remission


title: RA_remission_3


title: 301-001

description: ribodepleted RNA

value: glioblastoma tumor

value: Validation


title: mouse_SCI+CDTX_1

value: muscle


title: ATAC-seq ER-Hoxa9-Lys-GFP (-) E2 24h Rep 1

value: (-) E2 for 24 hours then +E2 add-back for 96 hours


title: RA_remission_2


title: RA_severe_3

value: severe rheumatoid arthritis


title: ATAC-seq ER-Hoxa9-Lys-GFP (+) E2 (untreated) Rep 1

value: (+) E2 (untreated)


title: Input DNA DRGM2 [NIPD2]

city: LYON

first: MARMIGERE

last: FREDERIC

address: 32/34 Av. Tony Garnier

department: Institut de génomique fonctionelle de Lyon

country: France

institute: CNRS

description:
processed data file:
Macs14_DRGM2_versus_NIPD2_model-s_peaks.bed
Macs2_DRGM2_versus_NIPD2_model_peaks.narrowPeak

data_processing:
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's Conversion Software (bcl2fastq 2.17).
The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
Peaks were called using MACS version 1.4.2 and MACS 2.1.1.
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing the detected peaks

source_name: Dorsal Root Ganglia

growth_protocol: Animals were grown with ad libitum standard mouse pellet food and water and housed at room temperature with a 12h light/dark cycle. All procedures were conducted according to the French Ministry of Agriculture and the European Community Council Directive no. 86/609/EEC, OJL 358.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the Illumina ChIP Sample Preparation Kit.

tag: chip antibody

value: Dorsal Root Ganglia

tag: cell type

value: Sensory neurons


title: RA_severe_1


title: 003-031

description: ribodepleted RNA

tag: tissue

value: B

value: Non-responder


title: 003-029

description: ribodepleted RNA


title: Input DNA DRGM1 [NIPD1]

description:
processed data file:
Macs14_DRGM1_versus_NIPD1_model-s_peaks.bed
Macs2_DRGM1_versus_NIPD1_model_peaks.narrowPeak


title: hBMSCs, untreated

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

country: Italy

institute: Università Politecnica delle Marche

description: Human Bone Marrow Stromal cells (hBMSCs), untreated

data_processing:
Relative quantity (RQ) of each miRNA was calculated with using the global mean normalization method. RQs were reported in the ‘Matrix normalized’ table as 2-ΔCt, where ΔCt was Ct microRNA - mean Ct values of miRNAs obtained in the sample profiling. Fold changes of adipogenic differentiation/untreated were calculated as RQ(adipogenic differentiation)/RQ(untreated).
Matrix normalized: 'global mean normalized relative quantities'; Fold Change: 'FC of adipogenic differentiation/untreated'

label: FAM

label_protocol: About 150–200 ng of total RNA was reverse transcribed by priming with a mixture of looped primers using the manufacturer’s instructions (Megaplex RT primers Human Pool A v2.1, Thermo Fisher Scientific). Pre-amplification of cDNA was performed using TaqMan Preamp Master Mix (#4384266, Thermo Fisher Scientific) and Megaplex PreAmp Primers (10x), Human Pool A v2.1 (#4399233, Thermo Fisher Scientific). Pre-amplified cDNA was used for mature miRNA profiling by RT-PCR instrument equipped with a 384-well reaction plate (7900 HT, Applied Biosystems) and TaqMan Array Human MicroRNA Cards v2.0 pool A (#4398977, Thermo Fisher Scientific) containing 367 different human miRNA assays in addition to selected small nucleolar RNAs.

growth_protocol: Human Bone Marrow Stem cells (hBMSCs) were purchased from Lonza (Allendale, NJ, USA) and maintained in α-MEM (Euroclone, 20016, Milano, Italy) supplemented with 10% fetal bovine serum (FBS) (Lonza) and 1% penicillin/streptomycin (f) at 37 °C in a humidified atmosphere containing 5% CO2/95% air. Experiments were performed using hBMSCs up to the fifth passage.

extract_protocol: Total RNA was recovered from hBMSCs using Total RNA Purification Kit purchased from Norgen (#37500, Norgen Biotek, Thorold, ON, Canada) that allows isolation of both microRNAs and mRNAs. RNA was used immediately or stored at -80°C until analysis by Real Time (RT) - PCR.

treatment_protocol: For adipogenic differentiation hBMSCs were seeded at 5 × 10^3 cells/cm2 on six-well plates in AD containing complete α-MEM, 2 mM l-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% FBS supplemented with 0.5 μM dexamethasone, 5 μg/ml insulin, 0.2 mM indomethacin, and 0.45 mM isobutylmethylxantine (Sigma-Aldrich, St. Louis, MO, USA). After 24-h FasL and/or neutralizing anti-Fas antibody was added to the cultures. AD medium and treatments were changed twice a week until the end of the experiment. BM–MSCs cultured in complete α-MEM without adipogenic supplements were used as control. Alternatively, 24 h after seeding 25 ng/ml FasL was added to α−MEM for 2 days; floating apoptotic cells were then removed and the medium replaced with AD supplemented with 25 ng/ml FasL, with or without ZB4 anti-Fas antibody, for 14 days.

value: 14 days

tag: cell provider

value: Lonza (Allendale, NJ, USA), cat no. #PT-2501


title: hBMSCs, adipogenic differentiation

description: Human Bone Marrow Stromal cells (hBMSCs), adipogenic differentiation


title: APL2

city: Bologna

first: Valentina

last: Indio

state: Bologna

address: via Giuseppe Massarenti,11

institute: University of Bologna

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using TopHat v.2.0.9
Count per million (CPM) were calculated using htseq-count version 0.6.1p1 using the annotation from Ensembl v.81.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count per million (CPM) values

source_name: bone marrow

extract_protocol:
RNA was extracted from bone marrow using the RNeasy Mini Kit (Qiagen), and cDNA libraries were synthesized from 500ng total RNA using the TruSeq Stranded mRNA kit (Illumina). Whole transcriptome sequencing was carried out at paired end mode on a Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age (months)

tag: Sex

value: M

value: acute promyelocytic leukemia lacking PML/RARA fusion


title: 003-024

description: ribodepleted RNA

tag: trial arm

tag: experimental set

tag: patient response

value: Responder


title: ChIPseq-Adult-DRG [DRGM2]

value: Meis1/2/3 antibody (Millipore, 05–779)


title: 003-023

description: ribodepleted RNA


title: mouse_SCI+CDTX_2

description:
9257636011_B
Excluded from final analysis. "matrix_normalized_final.txt" did not include this sample

value: SCI+CDTX

value: 2 days post surgery

value: Female


title: 201119L17_exp201103_MK918_SCD_1NMPP1-10min_AB03

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
base calling
read alignment, ChIP-seq data Bowtie 1.0.1
bigWig file generation custom code
custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

organism: Saccharomyces cerevisiae

extract_protocol:
Cells were fixed with 1% formaldehyde (30 minutes), quenched with 0.125 M glycine (5 minutes), washed twice in cold PBS, pelleted, snap-frozen and stored at −80°C. Pellets were lysed in 300 µL FA lysis buffer (50 mM HEPES–KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF, Roche protease inhibitor) with ∼1 mL ceramic beads using a Fastprep-24 (MP Biomedicals). The lysate was then collected and sonication to ~200bp fragments. Cell debris was then pelleted and the supernatant retained for ChIP. For each ChIP reaction, 30 µL Protein G Dynabeads (Invitrogen) were blocked (PBS + 0.5% BSA), prebound with 5-10 µL anti-V5 antibody (SV5-Pk1, BioRad Cat# MCA1360G) or  anti-FLAG antibody (M2, SIGMA Cat# F1804) and washed once with PBS before incubation with supernatant (4°C, overnight). Dynabeads were then washed (5 minutes per wash) twice in FA lysis buffer, twice in high-salt (500 mM NaCl) FA lysis buffer, twice in ChIP wash buffer (10 mM TrisHCl pH 7.5, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF) and once in TE wash buffer (10 mM TrisHCl pH 7.5, 1 mM EDTA, 50 mM NaCl). DNA was eluted in ChIP elution buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 1% SDS) at 65°C for 15-20 minutes. Eluted DNA was incubated to reverse crosslinks (65°C, 5 hours), before treatment with RNAse A (37°C, 1 hour) and then Proteinase K (65°C, 2 hours). DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Indexed sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB, # E7645) and pooled before paired-end (2x150 bp) Illumina sequencing

tag: tagged protein

tag: chip-antibody

value: anti-Rpb3 antibody (1Y26, Bioledgend #665004)


title: RA_severe_2

value: PBMC

tag: disease state


title: Input Replicate 2 [731 2020]

first: Oscar

last: Reina Garcia

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

data_processing:
Illumina 50 bp single-end RIP-Seq reads for CPEB4 IP, Input and IgG samples were aligned against Mus musculus mm10 UCSC rRNA sequences (October 2016) using Bowtie version 1.2.3 with options –n 2 –m 1 in order to detect potential rRNA contamination. Afterwards, non-rRNA sequences (Bowtie unaligned reads) were aligned against Mus musculus mm10 UCSC genome using Bowtie2 2.2.2 with options –N 1.
The Rsubread package version 1.32.4 was used to obtain read counts at 3’UTR level using 3’UTR mm10 annotation from Ensembl Biomart, March 2017 Archive, using the featureCounts function with options allowMultiOverlap=TRUE, minMQS=1.
Potential CPEB4 targets in IP samples were obtained using DESeq2 version 1.22.1 with lfcShrink normal foldchange estimates, with biological replicate as covariate, and using thresholds FC|Ip/Input|>1.5 and Benjamini-Hochberg adjusted pvalue < 0.05. Interaction analysis using IgG signal was used to further refine candidate CPEB4 binding site selection, with thresholds FC |(IP/Input) / (IgG/Input)|>1.5 and pvalue < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Excel XLSX file with sample quantification at mm10 3'UTR level and DESeq2 v1.22.1 analysis results for Main and Interaction effects.

source_name: Input

growth_protocol: 3T3-L1 predipocytes were cultured until confluence. Once reached 100% confluence preadipocytes undergo differentiation process with induction media followed by differentiation media until day 8 of differentiation. At day 8 of differetiation mature adipocytes were treated with a mixed of free fatty acids for 24h

extract_protocol:
Protein extract was obtained from  cells with cold RIPA lysis buffer supplemented with a protease and phosphatase inhibitor cocktail. RNA was isolated and purified from mouse tissue and cells using RNAspin Miki Kit (Quiagen).
Poly A purification (New England Biolabs, catalog # E7490) was the only performance of Input samples in only one step of purification. Library generation was done with the kit NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, catalog # E7770), following manufacturer´s instructions and 12/18 cycles of amplification.

treatment_protocol: Induction Media: 0.5mM IBMX, 1uM dexamethasone, 10ug/mL insulin and  2uM rosiglitazone on DMEM/F12 media until day 2. Diferentiation media: DMEM/F12 supplemented with 10ug/mL of insulin.  FFA treatment: FFA  to a final concentratipm of 500uM (300uM of Palmitic acid, 100uM Oleic Acid and 100uM Linoleic Acid)

tag: cell line background

value: immortalized cell line

tag: rip- antibody


title: 003-036

description: ribodepleted RNA

value: glioblastoma tumor

value: Discovery


title: 201119L15_exp201103_MK918_SCD_1NMPP1-01min_AB03

tag: strain


title: 002-075

description: ribodepleted RNA

value: D

value: Validation


title: 201119L16_exp201103_MK918_SCD_1NMPP1-03min_AB03


title: 003-016

description: ribodepleted RNA

value: B

value: Non-responder


title: 201119L14_exp201103_MK918_SCD_DMSO_AB03


title: 003-019

description: ribodepleted RNA


title: 201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03


title: IP CPEB4 Replicate 2 [730 2020]

source_name: IP CPEB4


title: 201119L13_exp200916_MK918_SCD_1NMPP1-10min_AB03


title: 002-074

description: ribodepleted RNA


title: 201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03


title: IP CPEB4 Replicate 1 [727 2020]


title: 002-069

description: ribodepleted RNA


title: 002-070

description: ribodepleted RNA


title: 201119L10_exp200916_MK918_SCD_DMSO_AB03


title: ChIPseq-E16-DRG [DRGM1]

value: Dorsal Root Ganglia

value: Sensory neurons


title: 002-067

description: ribodepleted RNA


title: Input Replicate 4 [398 2020]


title: IP IgG Replicate 1 [726 2020]

source_name: IP IgG

value: anti-IgG


title: IP CPEB4 Replicate 4 [397 2020]


title: 002-066

description: ribodepleted RNA


title: 201119L06_exp201104_MK978_SCD_1NMPP1-01min_AB107

data_processing:
read alignment, ChIP-seq data: Bowtie 1.0.1
bigWig file generation: custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

value: anti-FLAG antibody (M2, SIGMA Cat# F1804)


title: IP IgG Replicate 2 [729 2020]


title: 201119L07_exp201104_MK978_SCD_1NMPP1-10min_AB107


title: IP IgG Replicate 4 [396 2020]


title: Input Replicate 1 [728 2020]


title: Input Replicate 3 [395 2020]


title: 002-042

description: ribodepleted RNA


title: 210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107


title: 002-064

description: ribodepleted RNA


title: 002-030

description: ribodepleted RNA


title: IP CPEB4 Replicate 3 [394 2020]


title: 210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107


title: 210117L11_exp2101_MK978_SCD_DMSO_AB107


title: 002-026

description: ribodepleted RNA


title: 002-021

description: ribodepleted RNA


title: 201119L05_exp201104_MK978_SCD_DMSO_AB107


title: IP IgG Replicate 3 [393 2020]


title: PBMCs_BHD_patient 8

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

institute: University of Bari

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on SurePrint G3 Human gene expression 8X60K v2 microarray kit (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing:
Data extraction was performed using Agilent Feature Extraction software.
A p-value cut-off of 0.05 and a fold-change cut-off of 1.5 were applied to identify differentially expressed genes able to discriminate between the study groups.

source_name: PBMCs_bicarbonate dialysis

label_protocol: Labeled cRNA was generated using the Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: Twenty ml of whole blood were harvested from all patients at the time of enrolment. PBMCs were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden). Total RNA was extracted with the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). The concentration of total RNA was measured using NANODROP® spectrophotometer ND-1000 (Thermo Scientific, Waltham, MA, US) and RNA integrity was measured using the Agilent 2100 BIOANALYZER® (Agilent Technologies Deutschland GmbH, Waldbronn, Germany) along with the Agilent® RNA 6000 Nano Kit.

value: blood

value: PBMCs

value: bicarbonate dialysis (BHD)


title: PBMCs_BHD_patient 1


title: PBMCs_BHD_patient 7


title: 210117L10_exp2011_MK846_SCD_RAPA_AB107


title: PBMCs_BHD_patient 3


title: PBMCs_OL-HDF_patient 8

source_name: PBMCs_on-line hemodiafiltration

value: on-line hemodiafiltration (OL-HDF)


title: PBMCs_BHD_patient 4


title: 210117L09_exp2011_MK846_SCD_DMSO_AB107


title: PBMCs_BHD_patient 2


title: PBMCs_OL-HDF_patient 6


title: PBMCs_OL-HDF_patient 5


title: PBMCs_BHD_patient 5


title: 002-018

description: ribodepleted RNA

source_name: glioblastoma tumor

value: Responder


title: PBMCs_OL-HDF_patient 7


title: PBMCs_OL-HDF_patient 4


title: 201119L04_exp201103_MK918_SCD_1NMPP1-10min_AB107


title: PBMCs_BHD_patient 6


title: PBMCs_OL-HDF_patient 3


title: 002-014

description: ribodepleted RNA


title: 201119L03_exp201103_MK918_SCD_1NMPP1-03min_AB107


title: 201119L02_exp201103_MK918_SCD_1NMPP1-01min_AB107


title: A10: pDC_rep1

city: Planegg

first: Anne

middle: Barbara

last: Krug

state: Bavaria

address: Großhaderner Str. 9

department: Institute for Immunology

institute: LMU Munich

description: ATCAAA

data_processing:
Illumina RTA 1.18.66.3 was used for basecalling
Sequence reads were processed using the zUMIs pipeline (version 0.0.1, Parekh et al. 2018). Within zUMIs, barcode and UMI sequences were quality filtered, allowing 4 bases with Phred score below 20. Remaining reads were mapped to the mouse genome (build mm10) using STAR (version 2.5.2b72). Gene identities were obtained from Ensembl annotations (GRCm38 release 84). Count matrices were collapsed by UMI.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including UMI counts for each gene and each sample

source_name: Bone marrow

extract_protocol:
cells were FAC-sorted, total RNA extracted by means of silica spin columns and frozen.
modified bulk SCRB-seq (Parekh et al. 2016)

value: bone marrow

value: pDC

tag: well


title: 001-071

description: ribodepleted RNA

value: glioblastoma tumor


title: 001-076

description: ribodepleted RNA

value: Discovery


title: PBMCs_OL-HDF_patient 1


title: A7: CCR9lo-B220hi_rep1

description: CGGTGG


title: 200925L04_exp200916_MK918_SCD_NMPP1-10min_AB107


title: 001-064

description: ribodepleted RNA

value: D


title: A9: CCR9lo-B220hi_rep3

description: AAAGTT


title: 001-055

description: ribodepleted RNA

value: Validation


title: A11: pDC_rep2

description: TAAAGT


title: 200925L02_exp200916_MK918_SCD_NMPP1-01min_AB107


title: 001-078

description: ribodepleted RNA


title: A6: CCR9lo-B220lo_rep3

description: CCCACG


title: A5: CCR9lo-B220lo_rep2

description: GCTAGA


title: PBMCs_OL-HDF_patient 2


title: A4: CCR9lo-B220lo_rep1

description: TGTTTA


title: A8: CCR9lo-B220hi_rep2

description: GCTCGC


title: 200709L09_exp200625_MK846_SCD_DMSO_AB107


title: 200709L10_exp200625_MK846_SCD_RAPA-30min_AB107


title: 200526L73_exp2005_MK820_SCEG_AB101

value: anti-V5 antibody (SV5-Pk1, BioRad Cat# MCA1360G)


title: 001-043

description: ribodepleted RNA

value: Non-responder


title: 001-038

description: ribodepleted RNA


title: 200925L03_exp200916_MK918_SCD_NMPP1-03min_AB107


title: TG_E15

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

institute: shanghaitech university

data_processing:
based on HiSeq 2500 (Illumina) sequencing platform and Single-End was used
ChIP-seq reads were aligned to the mm10 genome and Burrows Wheeler Aligner (BWA) was used
Sequenced reads were trimmed for adaptor sequence using Skewer
Fragment sizes were predicted with MACS and normalized strand coefficient (NSC) was counted
peaks were called using MACS2 and MEME and Dreme software were used in demonstrating Motif sequence
Genome_build: mm10
Supplementary_files_format_and_content: peak counts

source_name: cortex

extract_protocol:
Samples were sheared in 1×Hank’s balanced salt solution (HBSS) and fixed in 1% formaldehyde to link proteins to DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Specific antibody of H3K9me2 was used in immunoprecipitation and genomic DNA was purified.
All procedures followed the guidelines provided by Illumina Paired-End DNA Sample Prep Kit. Briefly, after purified from ChIP samples, DNA was end repaired and then added with A and adapter for amplification.

tag: developmental stage

value: embryonic day 15.5

value: cortex

tag: genotype/variation

tag: antibody


title: A2: pre-cDC_rep2

description: ATATAG

tag: tissue

tag: cell type

value: pre-cDC


title: 191002L06_exp190916_MK554_SCEG_AB101

tag: chip antibody


title: 200925L01_exp200916_MK918_SCD_DMSO_AB107

value: anti-FLAG antibody (M2, SIGMA Cat# F1804)


title: WT_E15

value: wildtype


title: 191002L08_exp190916_MK812_SCEG_AB101


title: A1: pre-cDC_rep1

description: AAAACT


title: 001-037

description: ribodepleted RNA

value: C


title: 001-047

description: ribodepleted RNA


title: 001-009

description: ribodepleted RNA

value: A


title: 001-046

description: ribodepleted RNA


title: 191002L04_exp190920_MK820_SCEG_AB101


title: 1794 PD1 8h Ab

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with HISAT (v0.1.5-beta) against themm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

source_name: brain

growth_protocol: Primary microglial cell cultures were prepared from mouse brains. After 5–8 days of primary cultivation, microglial cells were harvested by shake off.

extract_protocol:
Cells were  lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100-500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultivated for 2 or 8 hours with Amyloid-beta containing conditioned-medium.

tag: genotype

value: PD-1 KO

tag: time

value: 8 h

tag: treatment

value: Amyloid-beta


title: 191002L05_exp190918_MK532_SCEG_AB101


title: 1795 PD1 8h Ab


title: HEL ruxolitinib + pevonedistat rep 2

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab-separated values of gene expression (log 2 counts per million), fold change,  confidence intervals, and p-values.
Supplementary_files_format_and_content: Tab-separated values of raw counts.

source_name: HEL

growth_protocol: HEL cells were cultured in RMPI with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

treatment_protocol: HEL cells were treated in duplicate with DMSO, 0.5 µM ruxolitinib, 1 µM pevonedistat, or 0.5 µM ruxolitinib + 1 µM pevonedistat for 24 hours before harvesting.

value: JAK2 V617F mutant cell line

value: 0.5 microM ruxolitinib + 1 microM pevonedistat

tag: treatment duration

value: 24 hours


title: HEL ruxolitinib + pevonedistat rep 1


title: 1793 PD1 8h Ab


title: 191002L02_exp190916_MK555_SCEG_AB101

tag: tagged protein


title: 1792 WT 8h Ab

value: WT


title: 001-015

description: ribodepleted RNA

value: glioblastoma tumor

tag: trial arm

tag: experimental set

value: Discovery

tag: patient response

value: Responder


title: HEL pevonedistat rep 2

value: 1 microM pevonedistat


title: 190429L07_exp190221_MK627_SCEG_AB101

value: anti-V5 antibody (SV5-Pk1, BioRad Cat# MCA1360G)


title: HEL pevonedistat rep 1


title: P60 brain myelinating oligodendrocytes_RNASeq_n2

city: New York

first: Sarah

last: Moyon

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

data_processing:
100 ng of total RNA per sample were used for library construction with the Ultra-Low-RNA-Seq Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument for the FACS samples according to the manufacturer's instructions for 100 bp paired end read runs.
High-quality reads were aligned to the mouse reference genome (mm10), RefSeq exons, splicing junctions, and contamination databases (ribosome and mitochondria sequences) using the Burrows-Wheeler Aligner (BWA) algorithm. The read count for each RefSeq transcript was extracted using uniquely aligned reads to exon and splice-junction regions for each transcript.
The raw read counts were inputted into DESeq2 v1.2.5 (Anders and Huber, 2010) for calculation of normalized signal for each transcript and to ascertain differential gene expression with associated  p-values.
Differentially expressed genes were selected at a p-value < 0.05and  for fold change > 2 was used.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized signal for each transcript, for each sample.

source_name: Brain

extract_protocol:
Total RNAs were obtained from FAC-sorted P60 oligodendrocyte progenitor cells, P60 pre-myelinating oligodendrocytes and P60 myelinating oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: Post-natal day 60

value: Primary FAC-sorted NDRG1-eGFP+ cells


title: P60 brain myelinating oligodendrocytes_RNASeq_n1

tag: strain


title: P60 brain pre-myelinating oligodendrocytes_RNASeq_n3

value: Primary FAC-sorted PLP::GFP+ cells


title: P60 brain pre-myelinating oligodendrocytes_RNASeq_n2


title: P60 brain pre-myelinating oligodendrocytes_RNASeq_n1


title: 190429L06_exp190221_MK637_SCEG_AB101


title: 1790 WT 8h Ab


title: HEL ruxolitinib rep 2

value: 0.5 microM ruxolitinib


title: 190429L05_exp190220_MK554_SCEG_AB101


title: 1791 WT 8h Ab


title: HEL ruxolitinib rep 1


title: P60 brain oligodendrocyte progenitor cells_RNASeq_n2

value: Primary FAC-sorted PDGFRa::GFP+ cells


title: 1789 PD1 8h

value: PD-1 KO

value: no


title: P60 brain oligodendrocyte progenitor cells_RNASeq_n3


title: 190429L03_exp190220_MK645_SCEG_AB101


title: 190429L04_exp190220_MK653_SCEG_AB101


title: HEL DMSO rep 2

value: DMSO


title: P60 brain oligodendrocyte progenitor cells_RNASeq_n1


title: HEL DMSO rep 1

value: JAK2 V617F mutant cell line


title: shUHRF1_Rep3

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

institute: Washington University in St. Louis

data_processing:
Adapter ends were trimmed using FastQC
Reads were aligned to mm10 using STAR-align with default settings
Reads aligned to genes were counted using Htseq-counts with default settings
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Text files include gene counts; XLSX File includes differential expression analysis from DESeq2

source_name: Embryonic Dorsal Root Ganglia_shUHRF1

extract_protocol:
Invitrogen PureLink RNA Minikit with on-column Dnase treatment
Ribo-Zero Gold rRNA depletion then Clontech SMARTer cDNA Synthesis kit

treatment_protocol: Cells were either treated with shUHRF1 or shControl lentivirus as described

value: Embryonic day 13

value: Dorsal Root Ganglia

tag: knockdown


title: 1787 PD1 8h

value: 8 h


title: 190429L01_exp190220_MK555_SCEG_AB101


title: 1786 WT 8h

value: WT


title: shUHRF1_Rep2

tag: developmental stage


title: P60 brain myelinating oligodendrocytes_RNASeq_n3


title: 1785 WT 8h


title: 1784 WT 8h


title: shUHRF1_Rep1


title: shControl_Rep3

source_name: Embryonic Dorsal Root Ganglia_shControl

value: shControl


title: HC4

city: Shanghai

first: Ye

last: Zhao

address: 197 Ruijin Er Road

institute: Ruijin Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: excel file includes FPKM values for each Sample

source_name: Human esophagus biopsy from healthy conrols

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer’s instructions. RNA integrity was assessed on the Agilent Bioanalyzer 2100 system. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: esophagus

tag: disease

value: HC

tag: gender

value: Female

tag: age (yrs)

tag: bmi

tag: regurgitation

value: absent

tag: heartburn

tag: hiatus hernia

tag: smoking history

value: non-smoker

tag: drinking hisotry

value: non-drinker


title: eluturation-arrest-release-exp191107_small-50min_bio-rep2

data_processing:
read alignment, ChIP-seq Bowtie 1.0.1
read alignment, RNA-seq STAR-2.5.3a
custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

source_name: cells

extract_protocol:
cell pellets were lysed in 300 µL TRI Reagent (Zymo Research) by bead beating using a Fastprep 24 (4°C, settings: 5.0 m/s, 1 x 30 seconds). Cell debris was pelleted (13 krpm, 5 minutes) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research).
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing

tag: treatment

value: eluturation-arrest-release

tag: cell size

value: small

tag: time point

value: 50 min


title: HC6

tag: tissue


title: eluturation-arrest-release-exp191107_small-70min_bio-rep2

value: 70 min


title: HC5

value: Male

value: smoker

value: drinker


title: 1788 PD1 8h

tag: genotype

value: PD-1 KO

tag: time

value: no


title: eluturation-arrest-release-exp191107_small-40min_bio-rep2

tag: strain

value: 40 min


title: 1724 PD1 2h Ab

value: 2 h

value: Amyloid-beta


title: 1723 PD1 2h Ab


title: eluturation-arrest-release-exp191107_small-30min_bio-rep2

value: 30 min


title: HC3

value: esophagus

value: HC

value: Female


title: shControl_Rep2

tag: developmental stage

value: Embryonic day 13

value: Dorsal Root Ganglia

tag: knockdown

value: shControl


title: 1722 PD1 2h Ab


title: shControl_Rep1


title: 2b_CMV_bioreplicate_2

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: smallRNA IP

data_processing:
sRNAs were trimmed using Trim Galore.
All libraries were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. sRNAs were mapped with bowtie allowing 2 mismatches (-t -v2).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files were generated using Galaxy. For sRNA seq experiments reads were aligned with bowtie with the parameters -t -v2.

source_name: Rosette leaves

growth_protocol: Plants were grown under standard long day conditions at 22 °C, long day and 45% humidity

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies) following the manufacturer instructions. Total RNA was directly used for sRNA library preparation. PARE sequencing was obtained by purification with the NEB mRNA isolation kit (New England Biolabs).
sRNA libraries were produced using the TruSeq Small RNA Sample Preparation Kit (Illumina). PARE libraries were constructed according to Zhai et al (2014).

treatment_protocol:
Two leaves per Col-0 plant in the 4 rosettes leaves stage, 1.04 stage from Boyes et. al 2001, were rub-inoculated with 0.1 M Na2HPO4 containing the three RNAs that constitutes CMV (strain FNY) genome. These RNAs were previously obtained by in vitro transcription using the MAXIscript T7 Transcription Kit (ThermoFisher) and plasmids containing the individual genomic RNA sequences as the template for the transcription. Mock plants were rub-inoculated with Na2HPO4 buffer. Rosettes leaves from these Col-0 plants were taken at 30 dpi to perform sRNA-seq and PARE-seq. At the same time, Nicotiana benthamiana plants were infected with the same in vitro transcription products to obtain a reservoir of infected tissue, which was used to infect the ago mutants for RT-qPCR analysis and the Col-0 and ago7-HA for IP-sRNA-seq. For all the different analysis, samples were taken 30 dpi and plants were grown in the same chamber under the same conditions (long day, 22oC and 45% humidity).
sRNA IPs were performed using AGO1, AGO2, AGO5, HA and 2b antibodies from Agrisera (references: AS09 527, AS13 2682, AS10 671, AS12 2220 and AS16 3981, respectively) and following the protocol described in McCue et al. 2016.

value: Rosette leaves

value: wild type

tag: ecotype

value: Columbia 0

tag: molecule subtype

value: sRNA

tag: rip target


title: eluturation-arrest-release-exp191107_small-60min_bio-rep2

value: eluturation-arrest-release

value: small

value: 60 min


title: 1721 WT 2h Ab

value: WT


title: HC1

tag: disease

tag: gender

tag: age (yrs)

tag: bmi

tag: regurgitation

value: absent

value: non-smoker

value: non-drinker


title: NERD9

source_name: Human esophagus biopsy from patients with NERD

value: esophagus

value: NERD

value: present

tag: heartburn

tag: hiatus hernia

tag: smoking history

tag: drinking hisotry


title: eluturation-arrest-release-exp191107_small-00min_bio-rep2

tag: treatment

tag: cell size

tag: time point

value: 00 min


title: NERD8

tag: tissue

value: Female


title: 2b_CMV_bioreplicate_1

description: smallRNA IP

tag: genotype


title: eluturation-arrest-release-exp191107_medium-70min_bio-rep2

tag: strain

value: medium

value: 70 min


title: 1719 WT 2h Ab

tag: time

value: 2 h

value: Amyloid-beta


title: 1720 WT 2h Ab


title: A12: pDC_rep3

description: TTAATC

value: bone marrow

tag: cell type

value: pDC

tag: well


title: 2b_Input_CMV_bioreplicate_2

value: Rosette leaves

value: wild type

tag: ecotype

value: Columbia 0

tag: molecule subtype

value: sRNA

tag: rip target

value: none (input)


title: 2b_Input_CMV_bioreplicate_1


title: 1718 PD1 2h

value: PD-1 KO

value: no


title: eluturation-arrest-release-exp191107_medium-60min_bio-rep2

value: eluturation-arrest-release

value: 60 min


title: 1717 PD1 2h


title: AGO7_CMV_bioreplicate_2

description: smallRNA IP


title: NERD5

value: esophagus

tag: disease

value: NERD

tag: gender

tag: age (yrs)

tag: bmi

tag: regurgitation

value: present

value: absent

value: non-smoker

value: non-drinker


title: eluturation-arrest-release-exp191107_medium-50min_bio-rep2

tag: treatment

value: medium

value: 50 min


title: NERD6

value: Male

tag: heartburn

tag: hiatus hernia

tag: smoking history

value: smoker

tag: drinking hisotry


title: HC2

tag: tissue

value: HC

value: drinker


title: 1716 PD1 2h

tag: genotype

tag: time

value: 2 h


title: eluturation-arrest-release-exp191107_small-20min_bio-rep2

tag: strain

tag: cell size

value: small

tag: time point

value: 20 min