title: Input1

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

institute: Heidelberg University Hospital

data_processing:
Raw reads obtained from the Illumina libraries were processed with Trim Galore (version 0.6.4) and Cutadapt (version 2.10), and then mapped to the mouse genome (GRCm38.p6) using STAR (version 2.7.3a) in the two pass mode with default parameters.
Gene quantification was performed on uniquely mapped reads from the output of STAR with the software featureCounts (version 2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file with raw read counts of each gene from each sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596-026) according to the manufacturer's instructions, and RNA was subjected to DNaseI (Invitrogen, AM2222) treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hippocampus


title: Input2

status: Public on Dec 27 2020

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: IgG3


title: KO1

city: Guangzhou

first: Xiuqin

last: Bao

address: No. 1838, Guangzhou avenue north, baiyun district, Guangzhou

country: China

institute: Southern Medical University

data_processing:
The reads were aligned to the UCSC Homo sapiens reference genome hg19 with TopHat version 2.0.4, and multi-aligned reads were removed with SAMtools.
We then used HTSeq to generate mapping counts for the known annotated genes.
We used Cuffdiff to convert the counts into total FPKM values, which represented the gene expression levels.
DEGs between ERF KO and wild type were identified with the edgeR ver. 2.6.12 statistical package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: all_samples_FPKM.xls: Excel file includes FPKM values for each Sample.
Supplementary_files_format_and_content: DEG_between_WTandMT_in_Pre_QLFTest.txt: Tab-delimited text file

organism: Homo sapiens

source_name: ERF KO HUDEP-2

extract_protocol:
HUDEP-2 cells were harvested and total RNA was extracted 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.

tag: cell line

tag: cell type

value: umbilical cord blood cells derived

tag: genotype

value: ERF knockout


title: KO3


title: Murine utricle cells [Cell_4]

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

country: USA

institute: VUMC

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: csv file with raw read counts

source_name: utricle cells

extract_protocol:
RNA lysis buffer
Smart-seq2

value: Mix of C57BL/6 and FVB

tag: age

value: Wildtype

tag: well volume

tag: plate position

tag: sequencing pool

tag: enzyme

value: maxima

tag: qc outcome

value: passed


title: SCR1

source_name: WT HUDEP-2

value: wild type


title: KO2


title: Murine utricle cells [Cell_7]


title: SCR2


title: Camk2b3


title: Murine utricle cells [Cell_13]


title: IgG1


title: Camk2b1


title: S55.180504

city: Duarte

first: Defu

last: Zeng

state: California

address: 1500 East Duarte Road

department: Immunology & Theragnostics

institute: The Beckman Reseach Institute

description: 16S microbiome data, Uncultured Fecal Bacteria, ABX

library_source: genomic

data_processing:
For all 3 runs, Illumina Real Time Analysis (RTA v1.18.54) was used for image analysis for each cycle of sequencing.
For the 170228 and 180504 runs, RTA was also used for base calling.  For the 180921 run, there was file corruption of the automatically generated FASTQ files.  This was likely a data transfer / storage issue, since we could later recover valid read sequences.  However, bcl2fastq (v2.18.0.12) was used for base calling of the 180921 run.
All 3 runs had single-barcode libraries for the 16S samples.  170228 and 180921 were 301+6+301 runs.  180504 had a mixed barcode design (these 16S barcodes were still 6 bp, but the overall run was 301+8+8+301).
mothur was used to merge paired-end reads and quality filter (using the make.contigs and screen.seqs functions, respectively; screen.seqs was run with the maxambig=0 parameter)
Custom code was used to filter for merged reads within the expected range (350-375 bp )
mothur was used to make genus-level classification (using classify.seqs, with parameter cutoff=80)
Genome_build: The SILVA database as formatted and provided on the mothur website (silva.bacteria.fasta and silva.bacteria.rdp.tax) was used as the reference for classification and taxonomy annotations (created on 4/22/2012).
Supplementary_files_format_and_content: GEO_abundance.txt:  Proportions of genus levels counts (does not sum to 1 or 100% per sample, in order to account for unclassified reads).  Proportion / Frequency / Abundance Values (length-filtered, but shows fraction of unclassified reads).
GEO_read_counts-per-20k-reads.txt:  Raw read counts from down-sampled reads (rarified to 20,000 paired-end reads).

molecule: genomic DNA

source_name: Uncultured Fecal Bacteria, ABX

growth_protocol:
“liver” samples in the 180504 run means we culture the liver suspension in the plate and extract the DNA from the plate bacteria colony. Other  “IFNgKO.aCD4+IgG” DNA samples in the 180504 run is mouse stool (along with all of the other groups).
Samples under ABX treatment don’t pass the length filtered criteria to be included in the abundance table, which may because the antibiotics killed most of the bacteria.

extract_protocol:
DNA was extracted DNeasy PowerSoil Kit (QIAGEN) according to manufacturer’s protocol.
Primers were used to amplify the V45 region of the 16S ribosomal RNA (with forward primer ACACTCTTTCCCTACACGACGCTCTTCCGATCTAYTGGGYDTAAAGNG and reverse primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCGTCAATTYHTTTREGT)
DNA-Seq, 16S Amplicon-Seq

treatment_protocol:
GVHD model 1: lethally irradiated WT BALB/c recipients were given splenocytes contained T cells (1.5x106) from WT-C57BL/6 donors or IFN-g-/- C57BL/6 donors, with TCD-BM (2.5x106) from WT C57BL/6 donors. Allogeneic recipients were also treated with depleting anti-CD4 mAb (500µg/mouse) immediately after HCT.  Recipients were intraperitoneal injected anti-mouse IL-22 (Genentech Clone 8E11, isotype mouse IgG1) from day 0, 150ug/mouse, every other day until day 8 after HCT. Certain control groups also received isotype control IgG1 mAb. For ABX group, recipients were gavaged with combined four antibiotics including Ampicillin(1g/L), Neomycin(1g/L), Metronidazole(1g/L), and Vancomycin (0.5g/L) (4ABX) or PBS (250µl/mouse/day) from days 0-7 following HCT.
GVHD model 2:  lethally irradiated WT or Reg3g-/- C57BL/6 recipients were given splenocytes contained T cells (2.5x106) from IFN-g-/- BALB/C donors, with TCD-BM (2.5x106) from WT BALB/C donors. Allogeneic recipients were also treated with depleting anti-CD4 mAb (500µg/mouse) immediately after HCT.

tag: study

value: BMT

tag: group

value: ABX

tag: treatment

tag: bmt donor

value: IFNg-KO C57BL/6

tag: bmt recipient

value: WT BALB/c + antibotics + aCD4

tag: gvhd

value: No

tag: sequencing batch

tag: other batch


title: S58.180504


title: S3.180921

description: 16S microbiome data, Uncultured Fecal Bacteria, WT BMT

source_name: Uncultured Fecal Bacteria, WT BMT

value: WT BMT

value: IFNg-KO BALB/C

value: WT C57BL/6

value: Yes


title: S36.180504


title: S4.180921


title: S45.180504


title: S49.180504


title: S46.180504


title: S56.180504


title: W6.180921


title: S1.180921


title: IgG2

tag: strain

tag: tissue

value: hippocampus


title: Camk2b2


title: S44.180504


title: W9.180921


title: S43.180504


title: W8.180921


title: W7.180921


title: S48.180504


title: W3.180921


title: K9.180921

description: 16S microbiome data, Uncultured Fecal Bacteria, Reg3g-KO BMT

source_name: Uncultured Fecal Bacteria, Reg3g-KO BMT

value: Reg3g-KO BMT

value: Reg3g ko C57BL/6


title: S6.180921


title: W5.180921


title: K7.180921


title: K5.180921


title: K2.180921


title: W1.180921


title: W4.180921


title: W2.180921


title: S5.180921


title: K4.180921


title: K3.180921


title: K8.180921


title: K6.180921


title: S19.0425.180504

description: 16S microbiome data, Uncultured Fecal Bacteria, IFNg ko donor

value: WT-SPL

value: IFNg ko donor

value: WT BALB/c + aCD4 + IgG

value: B


title: S53.180504

description: 16S microbiome data, Uncultured Fecal Bacteria, WT donor

source_name: Uncultured Fecal Bacteria, WT donor

value: WT donor

value: A


title: K1.180921


title: S65.180504

description: 16S microbiome data, Uncultured Fecal Bacteria, BALB/C

source_name: Uncultured Fecal Bacteria, BALB/C

value: BMT

value: Untreated BALB/c

value: BALB/C


title: S74.180504


title: S79.180504


title: S76.180504


title: S78.180504


title: S77.180504


title: S40.180504

value: ABX

value: IFNg-KO C57BL/6

value: WT BALB/c + antibotics + aCD4

value: No


title: S66.180504


title: S47.180504


title: S51.180504


title: S39.180504


title: S52.180504


title: S54.180504

value: WT C57BL/6


title: S60.180504

source_name: Uncultured Fecal Bacteria, IFNg ko donor

value: IFNg-/- SPL+IgG

value: IFNgKO C57BL/6

value: Yes


title: S63.180504


title: S32.180504


title: S62.180504


title: S34.180504


title: S35.180504


title: S88.180504

description: 16S microbiome data, Uncultured Fecal Bacteria, Anti-IL22

source_name: Uncultured Fecal Bacteria, Anti-IL22

value: IFNg-/- SPL+anti-IL-22


title: S30.180504

value: IFNg ko donor


title: S18.0425.180504

value: WT-SPL

value: WT BALB/c + aCD4 + IgG


title: S50.180504


title: S6.0425.180504

value: WT donor

value: B


title: S64.180504

value: BMT

value: A


title: S89.180504


title: S85.180504


title: S61.180504


title: S86.180504


title: S87.180504


title: S75.180504

value: Untreated BALB/c

value: BALB/C


title: S13.180504

description: 16S microbiome data, Bacterial Colonies from Liver Suspension, KO liver

value: Bacterial Colony

value: Liver

value: KO liver


title: S14.180504

source_name: Bacterial Colonies from Liver Suspension, KO liver


title: S1.180504


title: S16.180504


title: S17.180504


title: S4.180504


title: S2.180504


title: S37.180504


title: S15.180504


title: S62.170228

description: 16S microbiome data, Uncultured Fecal Bacteria, cohouse.WT.aCD4

value: cohouse

value: Co-house WT SPL REC

value: WT C57BL/6

value: No


title: S57.170228

source_name: Uncultured Fecal Bacteria, cohouse.WT.aCD4


title: S51.170228

description: 16S microbiome data, Uncultured Fecal Bacteria, cohouse.IFNgKO.aCD4

value: Co-house IFNg KO SPL-Rec

value: IFNgKO C57BL/6


title: S61.170228


title: S59.170228


title: S52.170228

source_name: Uncultured Fecal Bacteria, cohouse.IFNgKO.aCD4


title: S64.170228


title: S63.170228


title: S55.170228


title: S58.170228


title: S18.170228

description: 16S microbiome data, Uncultured Fecal Bacteria, WT.aCD4

source_name: Uncultured Fecal Bacteria, WT.aCD4

value: WT-SPL


title: S13.170228

value: WT BALB/c + aCD4 + IgG


title: S12.170228


title: S20.170228


title: S14.170228


title: S17.170228


title: S3.180504

value: Yes


title: S16.170228


title: S11.170228


title: S15.170228


title: S42.170228

description: 16S microbiome data, Uncultured Fecal Bacteria, IFNgKO.aCD4+IgG

value: IFNg-/- SPL+IgG


title: S50.170228


title: S54.170228


title: S41.170228

source_name: Uncultured Fecal Bacteria, IFNgKO.aCD4+IgG

value: BMT


title: S43.170228


title: S40.170228


title: B. orientalis embryo, 9hr, 100 ug/mL heavy diesel particulate matter treatment, rep 2

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Clena up the adpater sequences with trimmomatic (0.39)
Map the reads to the cDNA references using kallisto (0.44.0)
Normalize with txtimport and limma
Call the differentially expressed genes with limma
Genome_build: Bombina_orientalis.a2020_08.cdna.fa.gz
Genome_build: XENLA_XB201901_tx_annot.fa.gz
Supplementary_files_format_and_content: Default output of kallisto (0.44.0)

molecule: polyA RNA

organism: Bombina orientalis

source_name: whole embryo

growth_protocol: Xenopus laevis and Bombina orientalis adult females were ovulated using 380 units of human chorionic gonadotropin (HCG) a day before. For B. orientalis, an adult male was also ovulated using 280 units of HCG a day before for natural mating. For X. laevis egg fertilization, a testicle was dissected from an adult male, ground, and sprayed on the squeezed X. laevis eggs. To remove the jelly layer, a 3% cysteine pH 7.9 solution was used for X. laevis embryos and a 3% cysteine pH 9.5 solution for B. orientalis embryos. Fertilized X. laevis embryos were grown in 1/3× MMR and fertilized. B. orientalis embryos were grown in sterilized water until used.

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher, 15596018) according to manufacturer’s protocol. To eliminate DNA, samples were purified using PCI/Ethanol purification and lithium chloride methods.
Library preparation were performed using a TruSeq stranded mRNA sample prep kit (Illumina, 20020595).

treatment_protocol: Xenopus laevis and Bombina orientalis embryos were washed using appropriate sterilized grown solution to remove mucus particles remained on epithelium. After washing, embryos were incubated in 100ug/ml heavy diesel particulate matter (PM) for 3 hours or 9 hours. Incubated embryos were lysed for further analysis.

value: PM100 treatment


title: B. orientalis embryo, 9hr, 100 ug/mL heavy diesel particulate matter treatment, rep 1


title: S60.170228


title: B. orientalis embryo, 3hr, 100 ug/mL heavy diesel particulate matter treatment, rep 2


title: B. orientalis embryo, 3hr, 100 ug/mL heavy diesel particulate matter treatment, rep 1


title: S32.170228


title: S53.170228


title: S34.170228


title: S36.170228


title: S49.170228

description: 16S microbiome data, Uncultured Fecal Bacteria, IFNgKO.aCD4+aIL22

value: IFNg-/- SPL+anti-IL-22

value: WT BALB/c + aCD4 + IgG + Anti-IL22


title: S39.170228


title: S33.170228


title: S31.170228


title: S46.170228

source_name: Uncultured Fecal Bacteria, IFNgKO.aCD4+aIL22


title: S35.170228


title: S45.170228


title: S37.170228


title: B. orientalis embryo, 9hr, control, rep 2

value: No treatment


title: S38.170228


title: OG2mES 0819

first: zheng

last: hui

address: Kaiyuan av.190

institute: GIBH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: embryonic stem cells

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

tag: cell type

value: embryonic stem cells

tag: passages

value: no

tag: treatment time

value: 0 days


title: 0826 Ips D8 Tet1CD DKG

source_name: cells during reprogramming induced by OKSM

value: DKG

value: 8 days


title: 0826 Ips D8 Tet1CD Vc

value: cells during reprogramming induced by OKSM

value: Vc


title: 0826 Ips D8 Tet1CD DMSO

value: DMSO


title: S47.170228

value: IFNgKO C57BL/6

value: No


title: S48.170228


title: B. orientalis embryo, 9hr, control, rep 1


title: 0826 Ips D8 Flag DKG


title: B. orientalis embryo, 3hr, control, rep 2


title: 0826 Ips D8 Flag Vc


title: 0826 Ips D8 Flag DMSO


title: STAT5_WT_D0_3

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v0.36).
Transcript quantification was performed by salmon (v0.10.2) using arguments '-l IU --validateMappings --rangeFactorizationBins 4 --useVBOpt --numBootstraps 30' using the UCSC mm10 known gene transcript assembly (v9).
Transcripts were summarized to a gene level using tximport (v1.8.0).
DESeq2 (v1.14.1) was used to calculate differential gene expression.
Supplementary_files_format_and_content: Text files are raw counts (1 count = 1 read pair) as quantified by salmon (v0.10.2) summarized to a gene level by tximport (v1.8.0). Also provided are gene IDs, gene name, and gene descriptions.

source_name: splenic NK cells

extract_protocol:
Cells (TCRb- CD3- NK1.1+ Ly49H+) were sorted and RNA was extracted using ARCTURUS PicoPure RNA Isolation Kit (Applied Biosystems; Thermo Fisher) per manufacturer's instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.705-2ng total RNA with RNA integrity numbers ranging from 6.5 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).

tag: genotype

value: WT

tag: replicate

tag: condition


title: STAT5_WT_D0_1


title: 0826 Ips D3 Tet1CD Vc

value: 3 days


title: 0826 Ips D3 Tet1CD DKG


title: STAT5_WT_D0_2


title: STAT5_WT_D2_3


title: 0826 Ips D3 Tet1CD DMSO


title: STAT5_CKO_D0_3

value: CKO


title: STAT5_WT_D2_1


title: STAT5_CKO_D0_2


title: 0826 Ips D3 Flag DKG


title: MEF+2DG

source_name: fibroblasts

value: fibroblasts


title: STAT5_WT_D2_2


title: 0826 Ips D3 Flag Vc


title: MEF+VC


title: OG2mES 0822


title: STAT5_CKO_D0_1


title: MEF+DMSO


title: 0826 OG2MEF


title: B. orientalis embryo, 3hr, control, rep 1


title: STAT5_CKO_D2_3


title: STAT5_CKO_D2_1


title: STAT5_CKO_D2_2


title: Stool [38]

description: 16S rRNA

data_processing:
The primary analyses, including real-time signal processing and base calling were processed by a built-in PacBio Blade Center through Sequel ICS, and result stream directly to SMRT Link (v8.0.0.80529).
The CCS reads (> 5 Minimum Number of Passes and 0.99 Minimum Predicted Accuracy) were produced by the Circular Consensus Sequences (CCS) module in SMRT Link (v8.0.0.80529).
The demultiplexing and the taxonomic classification analysis of the CCS reads were carried out using SBanalyzer (v2.4-2) of Shoreline Biome (Farmington, CT) based on Athena V2 database.
Genome_build: Athena V2
Supplementary_files_format_and_content: The Taxonomy.csv file contains the processed data (taxonomic  classifications from the CCS raw reads).

source_name: Stool

extract_protocol:
Microbial DNAs from 1-3 mg of mouse fecal samples were extracted and purified according to the manufacturer’s protocol of EXT3-16S DNA Purification and PCR Amplification Kit of Shoreline Biome (Farmington, CT), and the extended (~2,500 bp) region, which contains 16S rRNA gene, the adjacent Internally Transcribed Spacer (ITS) and part of the 23S gene, was amplified using barcoded primer sets in the same kit.
To construct the SMRTbell libraries, all reagents were provided by PacBio (Menlo Park, CA) SMRTbell Template Prep Kit 1.0. Equal molar quantities of the amplicons were pooled. According to a PacBio standard protocol (Amplicon template preparation and sequencing) the damage of the DNA templates was repaired and their ends were blunted. After ligating adapters, the failed libraries were degraded by treating exonucleases. To load the libraries onto Sequel, the polymerase complexes were produced and the sample plate containing the final loading dilution was loaded on the machine.
Mutiplexing EXT3-16S DNA libraries

treatment_protocol: Given WT  T cells depleted bone marrow cells  only

value: BALB/c

value: Wild type

value: T cells depleted bone marrow cells  only


title: Stool [37]

description: 16S rRNA


title: Stool [40]

description: 16S rRNA


title: Stool [39]

description: 16S rRNA


title: 0824 Ips D8 Tet1CD DKG


title: 0826 Ips D3 Flag DMSO


title: X. laevis embryo, 9hr, 100 ug/mL heavy diesel particulate matter treatment, rep 2

organism: Xenopus laevis

value: PM100 treatment


title: Stool [35]

description: 16S rRNA


title: 0824 Ips D8 Tet1CD Vc


title: X. laevis embryo, 9hr, 100 ug/mL heavy diesel particulate matter treatment, rep 1


title: X. laevis embryo, 3hr, 100 ug/mL heavy diesel particulate matter treatment, rep 2


title: Stool [34]

description: 16S rRNA


title: 0824 Ips D8 Tet1CD DMSO


title: Stool [36]

description: 16S rRNA


title: Stool [20]

description: 16S rRNA

treatment_protocol: Given WT donor T cells  and treated Dexamathosone (5mg/kg) at days 3,10, 15 and 20 after bone marrow transplantation

value: donor T cells

tag: agent


title: X. laevis embryo, 3hr, 100 ug/mL heavy diesel particulate matter treatment, rep 1


title: Stool [32]

description: 16S rRNA


title: Stool [21]

description: 16S rRNA

value: Dexamathosone (5mg/kg) at days 3,10, 15 and 20 after bone marrow transplantation


title: 0824 Ips D8 Flag Vc


title: 0824 Ips D8 Flag DKG

value: DKG


title: Stool [22]

description: 16S rRNA


title: X. laevis embryo, 9hr, control, rep 2

value: No treatment


title: Stool [19]

description: 16S rRNA


title: 0824 Ips D8 Flag DMSO

value: cells during reprogramming induced by OKSM

value: 8 days


title: Stool [33]

description: 16S rRNA


title: X. laevis embryo, 9hr, control, rep 1


title: S44.170228

tag: study

value: BMT

value: IFNg-/- SPL+IgG

value: WT BALB/c + aCD4 + IgG

value: Yes


title: Stool [17]

description: 16S rRNA


title: Stool [16]

description: 16S rRNA

treatment_protocol: Given WT T cells  and treated Dexamathosone (5mg/kg) at days 3 after bone marrow transplantation

value: T cells


title: Stool [15]

description: 16S rRNA

value: Dexamathosone (5mg/kg) at days 3 after bone marrow transplantation


title: Stool [14]

description: 16S rRNA


title: 0824 Ips D3 Tet1CD DKG

value: 3 days


title: X. laevis embryo, 3hr, control, rep 2


title: 0824 Ips D3 Tet1CD Vc

value: Vc


title: Stool [13]

description: 16S rRNA

value: BALB/c

value: Wild type


title: Stool [12]

description: 16S rRNA


title: Stool [10]

description: 16S rRNA

treatment_protocol: Given IL-22-/- donor T cells  and treated Dexamathosone (5mg/kg) at days 3,10, 15 and 20 after bone marrow transplantation

value: IL-22-/- donor T cells

value: Dexamathosone (5mg/kg) at days 3


title: 0824 Ips D3 Tet1CD DMSO

value: DMSO


title: Stool [11]

description: 16S rRNA


title: 0824 Ips D3 Flag DKG

value: DKG


title: Stool [18]

description: 16S rRNA

value: donor T cells

value: Dexamathosone (5mg/kg) at days 3,10, 15 and 20 after bone marrow transplantation


title: Stool [9]

description: 16S rRNA


title: Stool [8]

description: 16S rRNA


title: KO input

data_processing:
All clean reads passed quality control with FASTQC and were mapped onto hg19 with bowtie2.
After removal of duplicates with picard, the bam data were ranked, and an index was created with samtools.
We used MACS2 to generate peak calls with input as the control and set a 200-bp band width in the shifting model to denote the peak with p < 0.01.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bdg.tdf: tdf files were generated using the MACS.

extract_protocol:
Lysates were clarified from sonicated nuclei and ERF-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: umbilical cord blood cells derived

value: ERF KO

tag: chip antibody


title: Stool [7]

description: 16S rRNA


title: 0824 Ips D3 Flag Vc

value: cells during reprogramming induced by OKSM

tag: treatment


title: KO ERF

value: ERF (ab153726, Abcam)


title: Stool [6]

description: 16S rRNA


title: 0824 Ips D3 Flag DMSO


title: WT Input

value: WT


title: Stool [5]

description: 16S rRNA


title: Spt16-TAP IP_Normal Growth_Replicate1

status: Public on Dec 26 2020

city: Hyderabad

first: Ashutosh

last: Shukla

state: Telangana

address: Habsiguda X Road

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

data_processing:
Reads with phred score < 20 on 80% of the bases were filtered out with FASTX toolkit V0.0.13
Reads aligned to yeast genome using Bowtie 0.12.8 allowing unique alignments with 3 mismatches and taking the best stratum.
Reads are extended to ChIP fragment size (170bp)
Read coverage at each position in the genome is scaled to 1 million and normalized to total number of reads in the library.
Coverage at each base is bundled as .bedGraph files.
Genome_build: sacCer3
Supplementary_files_format_and_content: BEDGRAPH

organism: Saccharomyces cerevisiae

source_name: Log-phase cells in the 1X YEP with 2% dextrose

growth_protocol: Spt16-TAP strain was grown up to A600~0.8 in YEP medium at 30°C

extract_protocol: IP, Input and mock DNA samples were processed according to Illumina standard protocol for ChIP-seq

treatment_protocol: Cells were fixed with 1% formaldehyde for 30 min. and quenched with 0.125M Glycine

tag: antibody

value: ANTI-IgG Sepharose (GE Healthcare product code:17-0969-01, lot number:10055839)

tag: nutrient status

value: normal


title: 0824 OG2MEF

value: fibroblasts

value: no

value: 0 days


title: X. laevis embryo, 3hr, control, rep 1

value: No treatment


title: Spt16-TAP IP_Nutrient Starvation_Replicate1

source_name: Log-phase cells shifted to 0.15X YEP minus carbon source (2hours)

value: nutrient starvation


title: Spt16-TAP Input


title: Spt16-TAP Mock

value: Protein A Sepharose (GE Healthcare product code:17-1279-02, lot number:10204516)


title: Spt16-TAP IP_Normal Growth_Replicate2


title: Spt16-TAP IP_Nutrient Starvation_Replicate2


title: Root_RNAseq

city: Xi'an

first: Bo

last: Cao

state: Shaanxi

address: 620 West Chang'an Road, Changan District

institute: Shaanxi Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Scutellaria viscidula Bunge whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, et al., Nat Biotech, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Scutellaria viscidula

source_name: root

extract_protocol:
Total RNA was extracted from each collected tissues using CTAB RNA isolation method (Chang et al. 1993). Three replicates were sampled and mixed for RNA preparation. RNA samples were treated with RNase-free DNase (TaKaRa, Dalian, China) to eliminate genomic DNA contamination. Degradation of RNA was monitored on 1% agarose gels. Purity of RNA was checked using Nano Photometer spectrophotometer (Implen, CA, USA). The concentration of RNA was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total of 16.5 μg RNA was equally pooled from the collected tissues for cDNA library preparation. Library quality assessment, assembling, clustering and sequencing were performed following the method of Chen et al. (Chen et al. 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: in June

value: root


title: WT ERF


title: S45-3

city: Chengdu

first: xungang

last: wang

address: No.9 Section 4, Renmin Nan Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

description:
dorsal muscle of S45
Microhyla_fissipes_unigene.fasta
Microhyla_fissipes_merged_fpkm.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
The expression level of each unigene was expressed as fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: de novo assembly (.fasta file includes the sequences of all unigenes)
Supplementary_files_format_and_content: .txt file includes FPKM values for all Samples

organism: Microhyla fissipes

source_name: S45, dorsal muscle

growth_protocol: Tadpoles were fed with spirulina powder once daily

extract_protocol:
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then, PCR was performed with a Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 4000 platform by NovoGene (Beijing), and paired-end reads were generated.

value: Stage 45

tag: collection site

value: Shuangliu, Chengdu, China (30.5825o N, 103.8438o E)

value: dorsal muscle


title: Day 35_30 mGy

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 2.1.0 with parameters  -p 12 -q --dta-cufflinks.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuffdiff from the Cufflinks package using -p 12 --no-diff as parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: pluripotent stem cell

growth_protocol: Induced pluripotent stem cells derived from healthy human (iPS0063) were proliferated with 2 mL of mTeSR™1 (STEMCELL technologies, Singapore) in 6-well plate coated with matrigel. mTeSR™1 was changed every day. Confluent iPS cells were dispersed in the matrigel coated plate at the concentration of one fourth to one sixth. After the cultivation for two to three weeks, they were used for embryoid body (EB) formation. Nine thousand cells per well were transferred into 96-well polystyrene round bottom plates in mTeSR™1 supplemented with 10 μM of Y-27632 and 10 ng/ml of Noggin (day 0). On day3, the culture medium was replaced with EB differentiation medium. The culture medium was changed three times per week. The cells were irradiated with 30 or 180 mGy for 24 hours from day4 to day5. Then, on day10, the embryonic bodies were transferred to 24-well flat bottom culture dishes coated with laminin-511 for the second stage. During the differentiation, DMEM-F12 with B-27, N-2, L-glutamin, NEAA, DKK-1 at 10 ng/ml, DATP at 10μM, and DKK-1 at 10ng/ml was changed every two days until the day 35.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.  1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: developing retinal ganglion cells

value: 30 mGy irradiated


title: S45-2


title: Day 35_180 mGy

treatment_protocol: The cells were irradiated with 30 or 180 mGy for 24 hours from day4 to day5.

value: 180 mGy irradiated


title: S45-1


title: non-rejection_plasma_replicate 1

type: RNA

city: Shanghai

first: jie

last: hu

address: 180 Fenglin Road

institute: Zhongshan hospital, Fudan University

hyb_protocol: Each slide was hybridized with 100 ng Cy3-labeled RNA with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA) in a hybridization oven (Agilent Technologies) at 55°C and 20 rpm for 20 hours according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned by an XDR Scan (PMT100, PMT5) according to the protocols of the Agilent microRNA microarray system

data_processing: The microarray image data were converted into spot intensity values with Feature Extraction Software Rev. 9.5.3 (Agilent Technologies). The signal minus background values were exported directly into GeneSpring GX10 software (Agilent Technologies), and the raw data were normalized by the Quantile algorithm.

organism: Rattus norvegicus

source_name: non-rejection plasma

label_protocol: RNA was labeled with Cy3 according to the protocols of the Agilent microRNA microarray system

growth_protocol: Inbred male Lewis and BN rats weighing 200-250g were maintained in laminar flow cages in a specific pathogen-free animal facility with a standard diet and water.

extract_protocol: Total RNA was extracted from plasma samples with the mirVana PARIS miRNA Isolation Kit (Ambion, Austin, TX) and from tissue samples with the mirVana miRNA Isolation Kit (Ambion). RNA concentrations were determined with a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Waltham, MA)

treatment_protocol: Freshly drawn blood was collected on the 7thday after OLT in ethylenediaminetetraacetic acid (EDTA)-treated tubes. Within 30 minutes, the tubes were centrifuged at 820g for 10 min. Then, 1-ml aliquots of plasma were transferred to 1.5-ml tubes and centrifuged at 16,000g for 10 min to pellet any remaining cellular debris. Liver grafts of each animal were obtained and conserved in liquid nitrogen until use.

value: plasma

tag: gender

value: male


title: Day 35_0 mGy

value: no irradiated


title: non-rejection_plasma_replicate 2

tag: tissue


title: non-rejection_plasma_replicate 3


title: non-rejection_plasma_replicate 4


title: acute rejection_plasma_replicate 1

source_name: acute rejection plasma


title: non-rejection_graft_replicate 3

source_name: non-rejection graft

value: liver graft


title: acute rejection_plasma_replicate 3


title: acute rejection_plasma_replicate 2


title: non-rejection_graft_replicate 4


title: acute rejection_plasma_replicate 4


title: non-rejection_graft_replicate 1


title: Day 17_30 mGy

tag: cell type


title: S43-2

description:
dorsal muscle of S43
Microhyla_fissipes_unigene.fasta
Microhyla_fissipes_merged_fpkm.txt

source_name: S43, dorsal muscle

value: Stage 43


title: S43-3


title: acute rejection_graft_replicate 3

source_name: acute rejection graft


title: acute rejection_graft_replicate 2


title: acute rejection_graft_replicate 1


title: non-rejection_graft_replicate 2


title: Day 10_180 mGy


title: S43-1


title: Day 17_180 mGy


title: acute rejection_graft_replicate 4


title: Day 10_30 mGy


title: S40-3

description:
dorsal muscle of S40
Microhyla_fissipes_unigene.fasta
Microhyla_fissipes_merged_fpkm.txt

source_name: S40, dorsal muscle

value: Stage 40


title: S40-2


title: Day 17_0 mGy


title: Day 10_0 mGy


title: Day 6_180 mGy


title: Day 6_30 mGy


title: S40-1


title: H1

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Data were analyzed using Cell Ranger™ v3.0.1 pipelines and were visualized by Loupe™ Cell Browser v3.0.2 Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: csv format: includes mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.
*tar archives include cell-level data: matrix.mtx, barcodes.tsv and features.tsv
*matrix.h5 files include cell-level data in H5 matrix format
*molecule_info.h5 files include per molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene. Also contain data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.

source_name: Metaplasia

extract_protocol:
Mice were euthanized and the genital tract was extracted. Endocervix, junction and ectocervix were cut out with a sterile surgical knife. Tissue samples were washed thoroughly in sterile PBS (Gibco, # 14190-094) and minced with surgical scissors. Minced tissue was incubated in 0.5 mg/ml collagenase type II (Calbiochem, # 234155) for 45 mins at 37 °C in a shaker incubator. Tissue and dissociated cells were pelleted by centrifugation (7 min at 1000 g, 4 °C), supernatant discarded, cells resuspended in warm TrypLE express (Gibco, # 12604021) and incubated for 15 min at 37 °C in a shaker incubator. After dissociation, the cell and tissue pellet was resuspended in ADF (Invitrogen) medium and passed through a 40 µM cell strainer (BD Falcon, # 352340) to separate the single dissociated cells from tissue pieces. Cells were pelleted by centrifugation (7 min at 1000xg, 4 °C) and resuspended in PBS containing 0.04% w/v BSA (400 μg/ml) at a concentration of 500-1500 cells/μl.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.

tag: strain

value: BALB/c

value: Metaplasia

value: technical replicate 2


title: G12

value: technical replicate 1


title: Day 6_0 mGy


title: G11

source_name: Ecto-endo junction

value: Ecto-endo junction


title: S36-2

description:
dorsal muscle of S36
Microhyla_fissipes_unigene.fasta
Microhyla_fissipes_merged_fpkm.txt

source_name: S36, dorsal muscle

value: Stage 36


title: Day 3


title: G10

source_name: Ectocervix

value: Ectocervix


title: S36-1

value: Shuangliu, Chengdu, China (30.5825o N, 103.8438o E)

value: dorsal muscle


title: S36-3


title: G9

source_name: Endocervix

value: Endocervix


title: Day 0

value: developing retinal ganglion cells


title: Aged_aHFSCs

status: Public on Dec 25 2020

city: Tokyo

first: Hiroyuki

last: Matsumura

state: Bunkyo-ku

address: Room 213, Chemistry East Building, Department of Chemistry, 7-3-1 Hongo

department: Graduate School of Science

institute: The University of Tokyo

hyb_protocol: 1.3 μg Cy3 labeled cDNA were fragmented, and hybridized at 65°C for 17 hr to an Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (Design ID: 028005).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: For normalization of microarray data, intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features that were flagged as no errors (Detected flags) and excluded features that were not positive, not significant, not uniform, not above background, saturated or population outliers (Compromised and Not Detected flags).

source_name: Aged aHFSCs

label_protocol: Total RNA was isolated using a RNA easy micro Kit (Qiagen) according to the manufacturer’s instructions. cDNA samples were prepared from RNA using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA, USA) according to the manufacturer’s instructions. Amplified cDNAs were labeled with Cyanine 3 (Cy3) using a SureTag DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer's instructions.

extract_protocol: HFSCs (CD34(Hi)/ITGA6(Hi)/ScaI(-)), IFE (ITGA6(Hi)/ScaI(Hi)) and total epidermal cells were harvested from young and from aged mice. Dissociated cells were FACS-sorted by FACC ariaII and reserved into Buffer RLT (Qiagen) by FACS aria II.

treatment_protocol: RU486 topical treatments (2.5mg/mice for 5days at 8wo) or hair depilation by hand

tag: age


title: hCOL17A1_aHFSCs

source_name: hCOL17A1 aHFSCs

value: young (12w)

tag: genotype

value: hCOL17A1 tg


title: hCOL17A1-tHFSCs


title: hCOL17A1_IFE

source_name: hCOL17A1 IFE


title: Aged_hCOL17A1tHFSCs

source_name: Aged hCOL17A1tHFSCs


title: aPKCcKO_tHFSCs

description: Ru486 treated

source_name: aPKCcKO tHFSCs

value: aPKCλcKO (aPKCλ flox/flox,K15crePR)


title: Aged_hCOL17A1_IFE

source_name: Aged hCOL17A1 IFE


title: Col17a1cKO_aHFSCs

description: Ru486 treated

source_name: young COl17a1 cKO (K15) HFSCs, plucking 3days,(2.5mg RU486 treated for 5days)

value: Col17a1cKO (Col17a1 flox/flox,K15crePR)


title: Aged_IFE

source_name: Aged IFE


title: Cont_aHFSCs

description: Ru486 treated

source_name: young HFSCs, plucking 3days,(2.5mg RU486 treated for 5days)


title: Spinal cord_PBS_imatinib_sample_3

city: Solna

first: Manuel

last: Zeitelhofer

address: Biomedicum

department: MBB

country: Sweden

institute: Karolinska Institute

hyb_protocol: GeneChip® ST Arrays (GeneChip® Mouse Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: Scanning was done using the GeneChip® Scanner 3000 7G

data_processing: The raw data was normalized in Expression Console, provided by Affymetrix (http://www.affymetrix.com), using the robust multi-array average (RMA) method. Subsequent analysis of the gene expression data was carried out in the statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). In order to search for the differentially expressed genes between the X and Y groups, an empirical Bayes moderated t-test was applied using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg.

label: Biotin

source_name: vascular fragments of spinal cord, healthy, imatinib treated

label_protocol: 10 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA from the entire expressed genome according to the Nugen Technologies, Inc. protocols Ovation® Pico WTA System V2 (M01224v2) and Encore Biotine Module (M01111v5).

growth_protocol: Mice were supplied with a standard mouse diet and were housed in 12h light/dark cycle with free access to water and food.

extract_protocol: Total RNA extracted using Qiagen kit following manufacturer's instructions. RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA).

treatment_protocol: Mice were either treated with imatinib or PBS for 2 weeks twice per day.

tag: Sex

value: female

value: adult

value: imatinib for 2 weeks twice per day

value: spinal cord


title: Aged_tHFSCs

source_name: Aged tHFSCs


title: Spinal cord_PBS_imatinib_sample_2


title: young IFE

source_name: young IFE


title: 200517480058_R05C01

type: genomic

city: Barcelona

first: Nuria

last: Mendoza

address: C/Casanova 143, cellex 2 A

country: Spain

institute: IDIBAPS

description:
DNA from PF block
Meld = Model for End-stage Liver Disease

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC 850K using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Liver tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver blocks with the Recover All kit following the instructions

value: liver

value: male

tag: bmi

tag: ecocardio

value: No eco

tag: age, etiology, meld

value: 42, HCV+Alcohol, 15

tag: fvc

tag: disease state

value: Control


title: aPKCcKO_aHFSCs

description: Ru486 treated

source_name: aPKCcKO aHFSCs


title: Aged_hCOL17A1aHFSCs

source_name: Aged hCOL17A1aHFSCs


title: Col17a1cKO_tHFSCs

description: Ru486 treated

source_name: young Col17a1cKO(K15 promoter) HFSCs (2.5mg RU486 treated for 5days)


title: Cont_tHFSCs

description: Ru486 treated

source_name: young (12w) HFSCs (hair follicle stem cells), (2.5mg RU486 treated for 5days)


title: Spinal cord_PBS_healthy_sample_2

source_name: vascular fragments of spinal cord, healthy, PBS treated

tag: treatment

value: PBS for 2 weeks twice per day


title: Spinal cord_PBS_healthy_sample_1


title: Spinal cord_PBS_healthy_sample_3


title: Spinal cord_PBS_imatinib_sample_1


title: 200514040133_R04C01


title: Spinal cord_naive_sample_4 [naive.4]

source_name: vascular fragments of spinal cord, naive

treatment_protocol: Mice were either treated with imatinib or PBS starting from 2 days post MOG immunization until the end of the experiment twice per day.

value: naive

value: vascular fragments of spinal cord


title: Spinal cord_naive_sample_2 [naive.2]


title: 200514040133_R03C01

value: Positive

value: 50,Alcohol, 14

value: HPS


title: 200517480077_R03C01

value: 63, Alcohol, 17


title: 200517480058_R03C01

value: 53, Alcohol, 17


title: 200517480077_R05C01

value: female


title: Spinal cord_Imatinib_day32_sample_4 [day32.Imatinib.4]

source_name: vascular fragments of spinal cord, 32 days post MOG immunization, Imatinib treated

value: adult

value: Imatinib treated

tag: timepoint

value: 32 days post MOG immunization


title: Spinal cord_Imatinib_day13_sample_3 [day13.Imatinib.3]

source_name: vascular fragments of spinal cord, 13 days post MOG immunization, Imatinib treated

value: 13 days post MOG immunization


title: Spinal cord_Imatinib_day8_sample_4 [day8.Imatinib.4]

source_name: vascular fragments of spinal cord, 8 days post MOG immunization, Imatinib treated

value: 8 days post MOG immunization


title: Spinal cord_Imatinib_day8_sample_3 [day8.Imatinib.3]


title: Spinal cord_Imatinib_day32_sample_2 [day32.Imatinib.2]


title: Spinal cord_Imatinib_day32_sample_1 [day32.Imatinib.1]


title: 200517480058_R06C01

value: liver

value: male

value: No eco


title: Spinal cord_Imatinib_day13_sample_2 [day13.Imatinib.2]


title: 200517480077_R06C01

value: 61, Alcohol, 20


title: Spinal cord_naive_sample_1 [naive.1]

value: naive


title: 200517480058_R07C01


title: 200517480077_R04C01

value: 61, Alcohol, 10


title: 200517480077_R01C01

value: 59, Alcohol, 16

value: Control


title: Spinal cord_Imatinib_day13_sample_1 [day13.Imatinib.1]

value: vascular fragments of spinal cord


title: Spinal cord_Imatinib_day32_sample_3 [day32.Imatinib.3]


title: Spinal cord_PBS_day32_sample_4 [day32.PBS.4]

source_name: vascular fragments of spinal cord, 32 days post MOG immunization, PBS treated

value: PBS treated


title: Spinal cord_PBS_day32_sample_3 [day32.PBS.3]


title: Spinal cord_PBS_day32_sample_2 [day32.PBS.2]


title: Spinal cord_naive_sample_5 [naive.5]


title: Spinal cord_Imatinib_day8_sample_1 [day8.Imatinib.1]


title: Spinal cord_PBS_day13_sample_3 [day13.PBS.3]

source_name: vascular fragments of spinal cord, 13 days post MOG immunization, PBS treated


title: Spinal cord_PBS_day32_sample_1 [day32.PBS.1]


title: 200517480058_R08C01

value: Positive

value: HPS


title: Spinal cord_PBS_day13_sample_4 [day13.PBS.4]

value: female

value: adult


title: Spinal cord_Imatinib_day13_sample_4 [day13.Imatinib.4]

value: Imatinib treated


title: Spinal cord_PBS_day13_sample_2 [day13.PBS.2]

value: 13 days post MOG immunization


title: 3T3 H3K27ac ChIP-Seq

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Alignment of filtered reads to the mouse genome (mm10 assembly) was performed with bowtie2 (ver. 2.3.5.1), using the default parameters.
Aligned reads were filtered to remove sequences mapped to problematic regions, using the ENCODE blacklist downloaded from https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz
Peak calling was performed using macs2 (ver. 2.2.6), using a q-value cutoff 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by kallisto. Putative binding sites or chromatine modification regions are provided in a narrowPeak format, as repored by macs2.

source_name: Embryonic fibroblasts

growth_protocol: mESCs E14TG2a (E14) and NIH3T3 cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma-Aldrich, G5154), supplemented with 10% FBS (Pan-biotech, 2602-P290705), 1,000 U/ml LIF (ESGRO, ESG1106), 100 mM nonessential amino acids (Invitrogen, 11140-050), 2 mM L-glutamine (Invitrogen, 25030-081), and 50 µM 2-mercaptoethanol (Invitrogen, 31350-010).

extract_protocol:
Chromatin immunoprecipitation was done as described previously (Ding et al., 2015) using 20 μl of the antibody. DNA was fragmented to 200-500bp with a Covaris water-bath sonicator before the IP. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: chip antibody

value: anti-H3K27ac (Cell signaling, 8173S)


title: ESC RNA-Seq

data_processing:
Expression levels of individual transcripts were estimated by kallisto (ver. 0.46.1) using GENCODE transcriptome (release M19) as a reference.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by kallisto. Putative binding sites or chromatine modification regions are provided in a narrowPeak format, as repored by macs2.

source_name: Embryonic stem cells

extract_protocol:
For RNA extraction, typically 1-2 million cells were pooled down. Total RNA extraction was performed with the RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. To avoid contamination with genomic DNA an on-column DNase I digest was included as part of the RNase Mini kit protocol.
RNA libraries were prepared for sequencing using standard strand-specific Illumina protocols.


title: 3T3 RNA-Seq


title: 3T3 Input ChIP-Seq

data_processing:
Alignment of filtered reads to the mouse genome (mm10 assembly) was performed with bowtie2 (ver. 2.3.5.1), using the default parameters.
Aligned reads were filtered to remove sequences mapped to problematic regions, using the ENCODE blacklist downloaded from https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz
Genome_build: mm10
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by kallisto. Putative binding sites or chromatine modification regions are provided in a narrowPeak format, as repored by macs2.

extract_protocol:
Total genomic DNA was fragmented to 200-500bp with a Covaris water-bath sonicator. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.


title: Spinal cord_PBS_day13_sample_1 [day13.PBS.1]


title: 3T3 Ctr9-EGFP ChIP-Seq

value: Anti-GFP antibody, MPI-CBG


title: ESC Input ChIP-Seq (B)


title: ESC Nelfa-EGFP ChIP-Seq

data_processing:
Alignment of filtered reads to the mouse genome (mm10 assembly) was performed with bowtie2 (ver. 2.3.5.1), using the default parameters.
Aligned reads were filtered to remove sequences mapped to problematic regions, using the ENCODE blacklist downloaded from https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz
Peak calling was performed using macs2 (ver. 2.2.6), using a q-value cutoff 0.01 and a fixed fragment extension mode (200 bp). Sample "ESC Input ChIP-Seq (B)" was used as a control.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by kallisto. Putative binding sites or chromatine modification regions are provided in a narrowPeak format, as repored by macs2.


title: Spinal cord_PBS_day8_sample_4 [day8.PBS.4]

source_name: vascular fragments of spinal cord, 8 days post MOG immunization, PBS treated

value: 8 days post MOG immunization


title: ESC Pol2Ser5P ChIP-Seq

value: anti-RNAPII Ser5p (Cell signaling, 13523S)


title: ESC Input ChIP-Seq (A)


title: Spinal cord_PBS_day8_sample_1 [day8.PBS.1]


title: Spinal cord_PBS_day8_sample_3 [day8.PBS.3]


title: ESC H3K27ac ChIP-Seq

data_processing:
Alignment of filtered reads to the mouse genome (mm10 assembly) was performed with bowtie2 (ver. 2.3.5.1), using the default parameters.
Aligned reads were filtered to remove sequences mapped to problematic regions, using the ENCODE blacklist downloaded from https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz
Peak calling was performed using macs2 (ver. 2.2.6), using a q-value cutoff 0.01 and a fixed fragment extension mode (200 bp). Sample "ESC Input ChIP-Seq (A)" was used as a control.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by kallisto. Putative binding sites or chromatine modification regions are provided in a narrowPeak format, as repored by macs2.


title: Spinal cord_PBS_day8_sample_2 [day8.PBS.2]


title: H3K27me3_Rep1

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with bwa mem v0.7.12 using default parameters
peaks were called using MACS2 v2.1.1.20160309
for RING1B and CBX8 the narrowpeak caller was used with a q-value threshold of 0.01: RING1B_Rep1 vs Input_1, Ring1B_Rep2 vs Input_3, CBX8_Rep1 vs Input_3, CBX8_Rep2 vs Input_4
for H3K27Ac and H3K27me3 the broadpeak caller was used with a broad threshold of 0.1: H3K27me3 vs Input_1, H3K27me3_Rep2 vs Input_2, H3K27ac_Rep1 vs Input_5, H3K27ac_Rep2 vs Input_4
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are .csv files representing annotated peak calls from MACS2 and provided only for the antibody pulldown samples

source_name: Adult neural precursor

growth_protocol: Olfactory basal cells were isolated from adult olfactory epithelium on the basis of c-KIT expression (as described in Goldstein et al., 2016, Development). Cells were maintaned as adherent cultures on gelatin-coated tissue culture plastic. Medium consisted of NeuroCult Basal Medium (Stemcell Tech #05700), supplemented with NeuroCult Proliferation Supplement (Stemcell Tech #05701), EGF, FGF2, Heparin, Pen/Strep, BMP4, and SB431542.

extract_protocol:
Adherent cells were fixed in 1% formaldehyde. Cells were collected by scraping with a rubber policeman. Nuclei were isolated and sonicated by Bioruptor (Diagenode); lysates were clarified and chromatin were purified by protein-specific antibody.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs #E7103S)

value: WT olfactory basal cell line 1

tag: passage


title: Spinal cord_naive_sample_3 [naive.3]

value: naive


title: ESC Pol2Ser2P ChIP-Seq

value: anti-RNAPII Ser2p (Abcam, ab5095)


title: Input_1


title: Type7-H3K27me3-2

city: Memphis

first: Xiaolong

last: Chen

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using DeepTools python script bamCoverage normlized to FPKM. Scores represent normalized tag counts per million reads.

source_name: oocyte in promordial follicle

extract_protocol:
200-500 cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to illumina TruSeq DNA LT Sample Prep Kit( FC-121-2001, FC-121-2002)

value: oocyte in promordial follicle

value: histone H3K27me3 antibody (Diagnode)


title: Type4-H3K9me3-2

source_name: oocyte in secondary follicle

value: oocyte in secondary follicle

value: histone H3K9me3 antibody (Active Motif)


title: Type4-input


title: Type7-H3K9me3-2

source_name: oocyte in antral follicle

value: oocyte in antral follicle


title: Type2-H3K27me3-2


title: Type2-H3K27me3-1


title: Type4-H3K27me3-2


title: Type2-H3K9me3-2


title: Type7-H3K9me3-1


title: Type4-H3K27me3-1


title: T7OC.4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.0.13 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.3.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.

extract_protocol:
Harvested oocytes were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. cDNA were synthesized using primers with 24-nt poly(dT),then a universal tail was added to the second strand cDNAs. After 18-20 cyclesof PCR, the PCR product is purified by QIAquick PCR purification kit(28104).
The prepared cDNA are sheared using Covaris S220. Fragment ends are repaired using NEBNext End Repair Module(E6050), then a NEBNext dA-Tailing Module(E6053) was used to yield a protruding 3- 'A' base for ligation of Illumina's adapters.After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles. library fragments of 200-500bp were band isolated from an agarose gel.


title: T7OC.3


title: Type7-input


title: T7OC.2


title: T6OC.3


title: T7OC.1


title: T6OC.4


title: Spinal cord_Imatinib_day8_sample_2 [day8.Imatinib.2]

value: vascular fragments of spinal cord


title: T6OC.2


title: ESC Ctr9-EGFP ChIP-Seq


title: RING1B_Rep1


title: T5bOC.5


title: Type2-input


title: Type7-H3K27me3-1


title: Type4-H3K9me3-1


title: T5bOC.3


title: T5bOC.2


title: T5bOC.1


title: Type2-H3K9me3-1


title: T5aOC.3


title: T5aOC.2


title: T5aOC.1


title: T4OC.4


title: T4OC.2


title: T4OC.3


title: T3aOC.3

source_name: oocyte in primary follicle

value: oocyte in primary follicle


title: T3aOC.1


title: T2OC.4


title: T3bOC.5


title: T2OC.5


title: T3aOC.2


title: T4OC.1


title: T3bOC.3


title: T3bOC.4


title: T3aOC.4


title: T5bOC.4


title: T2OC.3


title: T1OC.1


title: T3aOC.5


title: T1OC.4


title: T4OC.5


title: T1OC.2


title: T2OC.1


title: T1OC.3


title: 2242-1_5_617_2

city: Los Angeles

first: Aaron

last: Gordon

state: CA

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

data_processing:
Paired end reads were mapped using STAR to hg38 with Gencode v25 annotations.
Gene expression levels were quantified using rsem (v1.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counts

source_name: human cortical spheroids

growth_protocol: hiPSC were cultured on inactivated mouse embryonic fibroblast feeders (EmbryoMax PMEF; Millipore) in DMEM/F12 (1:1, Life Technologies, 11330) containing 20% knockout serum (Life Technologies, 10828), 1mM non-essential amino acids (Life Technologies, 11140), 1:200 GlutaMax (Life Technologies, 35050), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, M3148), 1:100 penicillin and streptomycin (Life Technologies, 15070), and 10 ng/ml FGF2 (R&D Systems, 233-FB) diluted at 0.1% BSA in DPBS (Life Technologies, 14190). hCS were generated as previously described (Pasca, 2015). Intact hiPSC cells colonies were lifted using 0.7 mg/ml dispase and transferred to ultralow-attachment plastic dishes (Corning) in hiPSC cell medium supplemented with 5 μM dorsomorphin (Sigma-Aldrich), 10 μM SB-431542 (Tocris) both of which are SMAD inhibitors, and 10 μM Y-27632 (EMD Chemicals) which is a ROCK inhibitor. From day 2 (48 hours of differentiation), the medium supplemented with dorsomorphin and SB-431542 was changed daily. From day six until day 24, neural spheroids were grown in neurobasal-A (Life Technologies, 10888) neural medium supplemented with B-27 supplement without vitamin A (Life Technologies, 12587), 1:100 GlutaMax (Life Technologies), 1:100 penicillin and streptomycin (Life Technologies) and with 20 ng/ml EGF (R&D Systems, 236-EG) and 20 ng/ml FGF2 (R&D Systems, 233-FB). From day 25 to 42, the neural medium was supplemented with 20 ng/ml BDNF (Peprotech, 450-02) and 20 ng/ml NT3 (Peprotech, 450-03) and medium was changed every other day. From day 43 onwards, hCS were maintained in unsupplemented neural medium with medium changes every four days

extract_protocol:
Following extraction of total RNA, rRNA was depleted (RiboZero Gold, Illumina) and libraries were prepared using Truseq stranded RNA RiboZero Gold (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: M

tag: iPSc line

tag: differentiation day

tag: batch


title: 2242-1_17_303_2


title: 1205-4_17_303_2

value: F


title: 2242-1_5_652_2


title: 8858-1_17_303_2


title: 2242-1_2_280_2


title: 2242-1_2_161_2


title: 8858-1_3_100_2


title: 1205-4_3_100_2


title: 0307-1_16_70_2


title: 1205-4_16_70_2


title: 1205-4_2_280_2


title: 8858-1_16_183_2


title: 8858-1_2_280_2


title: 1205-4_2_587_2


title: 1205-4_16_183_2


title: 8858-1_2_161_2


title: 0307-1_2_50_2


title: 1205-4_2_50_2


title: 8858-1_2_50_2


title: 0307-1_2_119_2


title: 2242-1_2_70_2


title: 0307-1_2_25_2


title: 0307-1_2_280_2


title: 0307-1_2_70_2


title: 1205-4_2_70_2


title: 1205-4_2_245_2


title: 0307-1_2_126_2


title: H20961_2_371_2


title: 2242-1_2_25_2


title: 1205-4_2_392_2


title: 2242-1_5_614_2


title: 8858-3_2_392_2


title: 1205-4_2_419_2


title: 2242-1_11_423_2


title: 8858-1_7_336_2


title: 2242-1_7_336_2


title: 8858-1_8_273_2


title: 2242-1_8_273_2


title: 8858-1_6_163_2


title: 8858-1_9_218_2


title: LpTΔrelAΔspoTΔdksA_Late Stationary

first: Diego

last: Arambula

address: 615 Charles E Young Dr. South

institute: University of California Los Angeles

description:
Each SRR represents a biological replicate.
Sample-14
Sample-30

data_processing:
Sequencing of the cDNA libraries was carried out using the Illumina HiSeq 2000 system according to Illumina protocols.
Raw reads from RNAseq were processed per Illumina quality control tools with default settings
Filtered short reads were aligned using Burrows-Wheeler Aligner (v. 0.7.7-r441)
Gene counts from every sample were used to identify genes differentially expressed across relevant conditions (DeSeq2 with default parameters)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: NC_009494.2
Supplementary_files_format_and_content: Tab-delimited text files include gene counts and RPKM values for each sample.

organism: Legionella pneumophila

source_name: Bacterial strain

growth_protocol: Parental and mutant L. pneumophila Corby strains were routinely maintained in culture in yeast extract (PYG) broth, grown to indicated growth phases, pelleted and stored for analysis.

extract_protocol:
Bacterial pellets were flash frozen in a dry ice/methanol slurry, and RNA was harvested using RiboPure-Bacteria Kit (Ambion). 1µg total RNA was used in construction of sequencing libraries.
Libraries for whole transcriptome shotgun sequencing were constructed from isolated total RNA using Ovation Complete Prokaryotic RNA Seq Library System (NuGen) per manufacturer specifications

tag: strain

value: Corby

value: Deletion of genes relA, spoT, and delta_dksA

tag: growth phase

value: Late Stationary


title: 2242-1_6_163_2


title: 2242-1_13_149_2


title: LpTΔrelAΔspoTΔdksA_Early Exponential

description:
Each SRR represents a biological replicate.
Sample-13
Sample-29

tag: genotype

value: Early Exponential


title: LpTΔrelAΔspoTΔletA_Late Stationary

description:
Each SRR represents a biological replicate.
Sample-16
Sample-32

value: Deletion of genes relA, spoT, and delta_letA


title: LpTΔrelAΔspoTΔlrpR_Late Stationary

description:
Each SRR represents a biological replicate.
Sample-12
Sample-28

value: Deletion of genes relA, spoT, and delta_lrpR


title: LpTΔrelAΔspoTΔlrpR_Early Stationary

description:
Each SRR represents a biological replicate.
Sample-11
Sample-27

value: Early Stationary


title: LpTΔrelAΔspoTΔlrpR_Early Exponential

description:
Each SRR represents a biological replicate.
Sample-10
Sample-26


title: LpTΔrelAΔspoT_Late Stationary

description:
Each SRR represents a biological replicate.
Sample-6
Sample-22

value: Deletion of genes relA and spoT


title: 2242-1_1_463_1

tag: Sex


title: 2242-1_4_79_2


title: 8858-1_4_79_2


title: 8858-1_12_392_2


title: 8858-1_5_572_2


title: LpTΔrelAΔspoT_Early Stationary

description:
Each SRR represents a biological replicate.
Sample-5
Sample-21


title: 8858-1_10_226_1


title: 2242-1_14_99_1


title: 1205-4_1_75_1


title: LpTΔrelAΔspoT_Early Exponential

description:
Each SRR represents a biological replicate.
Sample-4
Sample-20


title: LpTΔlrpR_Early Stationary

description:
Each SRR represents a biological replicate.
Sample-8
Sample-24

value: Deletion of gene lrpR


title: 8858-1_1_463_1


title: 8858-1_14_52_1


title: LpTΔrelAΔspoTΔletA_Early Exponential

description:
Each SRR represents a biological replicate.
Sample-15
Sample-31


title: LpTΔlrpR_Early Exponential

description:
Each SRR represents a biological replicate.
Sample-7
Sample-23


title: LpTΔlrpR_Late Stationary

description:
Each SRR represents a biological replicate.
Sample-9
Sample-25


title: LpT_Late Stationary

description:
Each SRR represents a biological replicate.
Sample-3
Sample-19

value: Parental strain


title: 2242-1_10_226_1


title: 8858-3_14_52_1


title: 2242-1_15_25_1


title: LpT_Early Exponential

description:
Each SRR represents a biological replicate.
Sample-1
Sample-17


title: 1205-4_14_140_1


title: LpT_Early Stationary

description:
Each SRR represents a biological replicate.
Sample-2
Sample-18


title: 8858-1_1_75_1


title: 8858-1_15_25_1


title: 2242-1_1_75_1


title: 2242-1_14_288_1


title: 2242-1_14_140_1


title: Colorectal cancer 546T

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of transcripts

source_name: primary colorectal cancer

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: age

tag: gender

tag: msi status

value: MSS

tag: o.p. name

value: APR

tag: regression grade

value: moderate


title: Colorectal cancer 547T

value: LAR/PH

value: minimal


title: Colorectal cancer 551T

value: M

value: LAR


title: Colorectal cancer 549T

value: F

value: Ra-uLAR

value: near total


title: Rat E12

city: Tempe

first: Janet

middle: L

last: Neisewander

state: AZ

address: 427 E Tyler Mall

department: SOLS

institute: Arizona State University

description: miRNA

hyb_protocol: Sequence specific flurorescent reporter probes and biotinlyated capture probes were hybridized to ligated target nucleic acid complexes overnight at 65c for >12 h, followed by a a series of automated washes and immobilization onto a strepavidin lined cartridge for data collection

scan_protocol: Digital images from the cartridges were obtained over 4 h using the nCounter Digital Analyzer (CCD camera and microscope objective lens) using 555 FOV data resolution. Digital counts were tabulated and exported as comma separated values (CSV).

data_processing:
Differential expression analysis was performed using the R package “limma” to identify differences in miRNA expression between the high- and low-seeking groups. Briefly, normalization factors were calculated to scale the raw library sizes. Raw counts were converted to counts per million reads (CPM) for each miRNA.
Normalized probe counts (CPM)

source_name: nucleus accumbens shell

label_protocol: 100ng total RNA was used in a multiplexed annealing reaction to anneal specific miRNA tags followed by ligation and enzymatic purification to remove excess unincorporated tags in the assay, following manufacturer protocol

extract_protocol: Tissue was extracted following deep anesthetization with isoflurane. Whole brain tissue was flash frozen in methylbutane and stored in -80C freezer. 2mm coronal slices containing the striatum were cut and a punch of the nucleus accumbens shell was isolated.

tag: tissue

value: nucleus accumbens shell

value: sprague-dawley

value: male

tag: group

value: Isolated Housing During Abstinence - Low Cue Reactivity Group


title: abdominal aortic aneurysm tissue, Aly/REF_RIP-seq

city: Dalian

first: Yanshuo

last: Han

address: No.2 Dagong Load

institute: Dalian University of Technology

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse LncRNAs and mRNAs
Genome_build: HG19
Supplementary_files_format_and_content: Number of raw junction read

source_name: infrarenal abdominal aortic aneurysm tissue

extract_protocol:
RIP-seq was first performed using the Magna RIP™ RNA-binding Protein Immunoprecipitation Kit (Millipore, Massachusetts, USA), according to the manufacturer’s protocol. Briefly, magnetic beads coated with 10 μg of specific antibodies against Aly/REF (Abcam, Cambridge, UK) or normal IgG (Millipore, Massachusetts, USA) were incubated with prepared indicated cell lysates overnight at 4 °C. Washed RNA-protein complexes were treated with proteinase K digestion buffer. The coprecipitated RNAs were purified with phenol: chloroform: isoamyl alcohol and subsequently subjected to purity and concentration analysis using NanoDrop 2000c.
rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using (New England Biolabs, Inc., Massachusetts, USA). RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: infrarenal abdominal aortic aneurysm

tag: condition

value: non-rupture

tag: rip antibody

value: Aly/REF (Abcam, Cambridge, UK)


title: Rat E13

description: miRNA

value: Enriched Housing During Abstinence - Low Cue Reactivity Group


title: BH190126-1_treatment of electro-acupuncture

city: Tianjin

first: Jin

last: Huang

address: No.10 Poyang Lake Road, Tuanbo new town, Jinghai District

institute: Tianjin University of Traditional Chinese Medicine

description: Gene expression data of bone marrow

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label: biotin

source_name: zhenci(treatment of acupuncture)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After 2 weeks of treatment, the mice was anesthetized,  then the tibias were harvested, the epiphyses were cut and the bone marrow was collected by centrifugation，finally immediately frozen in liquid nitrogen (-195.79˚C) and transferred to a refrigerator at -80°C until they were used for experiments.

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

treatment_protocol: The bone marrow tissue were collected for further total RNA extraction.

value: bone marrow


title: abdominal aortic aneurysm tissue, IgG control_RIP-seq

value: IgG (Millipore, Massachusetts, USA)


title: BH190126-1_treatment of astragalus membranaceus

description: Gene expression data of bone marrow

source_name: huangqi(treatment of astragalus membranaceus)


title: BH190126-1_cisplatin

description: Gene expression data of bone marrow

source_name: pinxue(cisplatin)


title: Colorectal cancer 544T

value: ND

value: TAE

value: total


title: Rat E11

description: miRNA

value: Enriched Housing During Abstinence - High Cue Reactivity Group


title: BH190126-1_control

description: Gene expression data of bone marrow

source_name: con(control)


title: Rat E8

description: miRNA


title: Colorectal cancer 541T

value: F

value: MSS

value: RA-uLAR


title: Rat E10

description: miRNA

value: nucleus accumbens shell

value: Isolated Housing During Abstinence - High Cue Reactivity Group


title: Rat E7

description: miRNA

value: sprague-dawley

value: male


title: 833K-B4-3

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC beadchip array using standard Illumina protocol

data_processing: All DNA methylation analysis of MethylationEPIC array was performed in R  v.4.0.2. The IDAT intensity files were analyzed in minfi R package. Raw intensity values were  normalized with minfi FUNNORM.

source_name: Derived from 833K

extract_protocol: DNA was purified using the Qiagen DNeasy Kit according to standard instructions.  DNA samples in biological triplicate were sent to the Molecular Genomics/ Methylation Core at the University of Southern California.  Bisulphite treatment with the EZ DNA methylation kit (Zymo) was performed and bisulphite-converted DNA was processed as described in the Infinium FFPE Restoration guide.

value: testis

tag: cell type

value: Embryonic carcinoma

tag: cisplatin sensitivity

value: Cisplatin acquired resistant


title: Colorectal cancer 543T

value: Ra-uLAR

value: moderate


title: Colorectal cancer 539T

value: LAR

value: near total


title: Rat E6

description: miRNA


title: 833K-B4-2


title: 833K-2

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site; Abdomen

value: Cisplatin sensitive


title: Colorectal cancer 540T

value: APR

value: minimal


title: Rat E5

description: miRNA

value: Enriched Housing During Abstinence - Low Cue Reactivity Group


title: Colorectal cancer 538T

value: M

value: MSI-L

value: uLAR


title: 2102EP-B3-2

source_name: Derived from 2102EP


title: 2102EP-B3-3


title: NT2/D1-C2-2

source_name: Derived from NT2/D1


title: NT2/D1-C2-3


title: 2102EP-C1-1


title: 2102EP-B3-1


title: 2102EP-C1-2


title: Rat E4

description: miRNA

value: nucleus accumbens shell


title: 2102EP-C1-3


title: Colorectal cancer 536T

value: F

value: ND

value: TAE

value: total


title: 833K-3

value: testis

value: Embryonic carcinoma


title: Rat E3

description: miRNA

value: sprague-dawley

value: male


title: NT2/D1-C2-1

value: Cisplatin acquired resistant


title: 2102EP-2

source_name: Testicular embryonal carcinoma cell lines derived from retroperitoneal lymph node

value: Cisplatin sensitive


title: 2102EP-3


title: 833K-1


title: Colorectal cancer 535T

value: MSS

value: moderate


title: NT2/D1-3

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site, Lung


title: Rat E1

description: miRNA

value: Isolated Housing During Abstinence - High Cue Reactivity Group


title: 833K-B4-1


title: Colorectal cancer 534T

value: M

value: LAR


title: 2102EP-1


title: Colorectal cancer 533T

value: minimal


title: Rat 3_Glomerulus_D_removed_from_analysis

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
small RNA
sample removed from analysis

data_processing:
FastQ files were analyzed using the Partek Flow (version 6.0) software program (Partek, St. Louis, MO). Sequence was filtered for rRNA, tRNA, and mitochondrial DNA sequence using Bowtie 2 (v 2.2.5) using all default settings.
Remaining sequences of 18 bp or greater were retained and trimmed from both 5’ and 3’ ends if the Phred quality score was less than 20.
Samples were aligned with Bowtie version 1.0.0 to the rn6 reference index using up to a 1 base pair mismatch and seed length of 10. Samples that had less than 500,000 aligned counts were removed from further analysis (Rat 2, glomerulus).
Aligned sequences were then annotated to miRBase mature microRNAs v22 with the Partek E/M (expectation maximum) algorithm.
To identify those miRNA features with higher expression, counts were filtered out if the total raw counts for all samples were less than 100.  Raw counts were then normalized by "trimmed mean of M-values" (TMM).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited file contains TMM normalized count values for all samples and mapped featues (excluding features <100 total counts).

extract_protocol:
Frozen blocks containing kidney tissue were sectioned at 8 µm and adhered to glass slides. Serial sections were stained with rabbit anti-glutathione-s-transferase, sheep anti Tamm-Horsfall protein, or rabbit anti-aquaporin-2 (all from EMD Millipore) to identify proximal tubules, the TAL of the loop of Henle, and CD, respectively using the HistoGene LCM immunofluorescence staining kit (Thermo Fisher) and Alexa Fluor 488-conjugated donkey anti-rabbit or donkey anti-sheep secondary antibodies (Life Technologies) as appropriate. Additional serial sections were stained with a histochemical stain (HistoGene LCM frozen section staining kit; Thermo Fisher) to identify glomeruli. Nephron segments of interest were identified under fluorescence or light microscopy as appropriate and collected from the stained slides using an Arcturus XT Laser Capture Microdissection instrument onto CapSure LCM Macro caps (Thermo Fisher). RNA was isolated using the RNeasy Micro kit (Qiagen).  Samples were eluted in 20 µL RNase-free water, and RNA concentrations were determined using a NanoDrop 8000 at 260 nm.  RNA quality was assessed using an Agilent Bioanalyzer and an Agilent Small RNA Analysis Kit. Samples were stored at -80C prior to small RNA-sequencing conducted at the Laboratory Corporation, Inc (Seattle, WA; acquired by Covance).
Library construction was performed according to Illumina's TruSeq small RNA sample prep protocol (Illumina, San Diego CA). Each of the twelve samples was barcoded. Library quality was assessed using the Agilent Bioanalyzer DNA chip and quantified using Ribo Green dye and standard methods. Libraries will be subjected to HiSeq analysis to ensure library quality. Sample libraries were pooled and divided across two lanes (L001 and L002, see raw files) and two flow cells (AHG5GVBCX2 [A], AHGMTHBCX2 [B], BHG5GMBCX2 [C] or BHGFVCBCX2 [D]) to reach the targeted read count. Illumina HiSeq2000 analysis was performed using 50 bp single end reads, with a targeted read depth per sample of 40 million reads.

treatment_protocol: Kidneys from 3 naïve adult male Sprague-Dawley rats, 6 months old, were collected at necropsy into Optimum Cutting Temperature (OCT) embedding medium, frozen on dry ice and isopentane, and stored at ≤ -70 °C until use. All animal studies were conducted by the participating laboratories according to the national guidelines for care and use of laboratory animals and were approved by the Institutional Animal Care and Use Committee where the study was performed.

tag: rat id

value: Rat 3

value: Sprague Dawley

value: kidney

tag: kidney region

value: Glomerulus

value: 6 m

tag: exposure

value: naive


title: Colorectal cancer 532T

value: APR


title: Colorectal cancer 530T

value: RA-uLAR

value: near total


title: NT2/D1-1

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site; Lung

value: testis

value: Embryonic carcinoma


title: Rat 3_Glomerulus_C_removed_from_analysis

description:
small RNA
sample removed from analysis

tag: strain

value: male


title: Rat 3_Glomerulus_B_removed_from_analysis

description:
small RNA
sample removed from analysis


title: Rat E2

description: miRNA

value: nucleus accumbens shell

value: sprague-dawley


title: Colorectal cancer 537T

value: M

value: MSS

value: moderate


title: Colorectal cancer 529T

value: MSI-H


title: 1205-4_NA_50

description: cortical organoid

hyb_protocol: Hybridizatoin was performe according to manufacture's (Illumina) protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data was normalized using the noob method implemented in the minfi package in R

label_protocol: Labeling was performe according to manufacture's (Illumina) protocol

extract_protocol: DNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qigen, 80224

value: F

tag: iPSc line

tag: differentiation

tag: differentiation day

tag: batch


title: Colorectal cancer 527T

tag: age

tag: gender

tag: msi status

value: APR/TAH w/ BSO


title: Rat 2_Thick Henle Loop_D

description: small RNA

source_name: kidney_Thick Henle Loop

value: Rat 2

value: Sprague Dawley

tag: tissue

value: kidney

value: Thick Henle Loop

tag: Sex


title: 1205-4_NA_280

description: cortical organoid

source_name: human cortical spheroids


title: 8858-1_NA_161

description: cortical organoid


title: Colorectal cancer 524T

tag: o.p. name

value: Ra-uLAR

tag: regression grade

value: minimal


title: NT2/D1-2

value: testis

tag: cell type

value: Cisplatin sensitive


title: 8858-3_NA_652

description: cortical organoid


title: Colorectal cancer 521T

value: RA-uLAR

value: near total


title: Rat 3_Glomerulus_A_removed_from_analysis

description:
small RNA
sample removed from analysis

value: Rat 3

value: Glomerulus

value: 6 m

value: naive

value: male


title: 8858-3_NA_617

description: cortical organoid

value: M


title: Rat 3_Proximal Tubule_D

description: small RNA

source_name: kidney_Proximal Tubule

value: Proximal Tubule


title: 8858-1_NA_100

description: cortical organoid


title: 2242-1_NA_280

description: cortical organoid


title: Rat 2_Collecting Duct_D

description: small RNA

source_name: kidney_Collecting Duct

value: Rat 2

value: Collecting Duct


title: Rat 3_Collecting Duct_D

description: small RNA

value: Sprague Dawley

value: kidney


title: 0307-1_NA_280

description: cortical organoid


title: 2242-1_NA_25

description: cortical organoid


title: Rat 3_Thick Henle Loop_D

description: small RNA

value: Thick Henle Loop


title: Colorectal cancer 520T

source_name: primary colorectal cancer

value: MSS

value: RA-APR

value: moderate


title: 2242-1_NA_161

description: cortical organoid


title: Sample 2

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

data_processing:
Data was analyzed using Cell Ranger (v3.1.0) to perform demultiplexing, aligning reads, filtering, clustering, and gene expression analyses, using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files contain the unfiltered barcodes, matrix, and genes.

source_name: Omental Adipose Tissue

extract_protocol:
The cells were isolated from Human Omental Adipose Tissue using the Mesothelial Cell Isolation protocol.
According to 10x Genomics’ protocol, sequenced R1=26cycles R2=58cycles, i1=8cycles, i2=0 cycles

value: Omental Adipose Tissue

value: Mesothelial Cells


title: 0307-1_NA_50

description: cortical organoid


title: 1205-4_NA_303

description: cortical organoid

value: F


title: 0307-1_NA_25

description: cortical organoid


title: Sample 3


title: Rat 1_Thick Henle Loop_D

description: small RNA

value: Rat 1


title: 1205-4_NA_100

description: cortical organoid


title: 2242-1_NA_303

description: cortical organoid


title: 0307-1_12_70

description: cortical organoid


title: Sample 1


title: Rat 2_Proximal Tubule_D

description: small RNA

value: 6 m


title: BT89 treated with CB839 - replicate 3

city: Calgary

first: Ian

middle: James

last: Restall

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

description:
BT89_CB839_3
BT89_DMSO_CB839_processed.txt

data_processing:
Sequencing reads were pseudoaligned to the human NCBI RefSeq transcript database (assembly: GRCh37.p13) and quantified as transcripts per million (TPM) using the kallisto software package (ver. 0.42.4, https://pachterlab.github.io/kallisto).
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for transcripts in all samples, divided into two files based on the cell line used.

source_name: Brain tumor stem cell line

growth_protocol: BTSC lines were established from GBM surgical procedures following informed consent from patients and cultured as previously described in Chesnelong et al. Methods Mol Biol. 2019;1869:11–21.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, cat.# 74104), according to the manufacturer’s protocol.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina), according to the manufacturer’s protocol.

treatment_protocol: The BTSC lines BT67 and BT89 were treated with 1 μM CB-839 or equal volume DMSO (vehicle control) for 48-hours and pellets of three biological replicates from different days were collected.

tag: cell line

value: Brain tumor stem cell

tag: treatment


title: 8858-1_NA_280

description: cortical organoid


title: 2242-1_1_70

description: cortical organoid


title: 8858-1_NA_50

description: cortical organoid


title: 1205-4_NA_587

description: cortical organoid


title: 8858-1_NA_303

description: cortical organoid


title: 1205-4_1_245

description: cortical organoid


title: H20961_1_371

description: cortical organoid


title: BT89 treated with CB839 - replicate 2

description:
BT89_CB839_2
BT89_DMSO_CB839_processed.txt


title: Rat 1_Glomerulus_D

description: small RNA

tag: rat id

tag: kidney region

value: Glomerulus

value: naive

value: male


title: Rat 3_Glomerulus_D

description: small RNA

value: Rat 3

tag: strain

tag: exposure


title: BT89 treated with DMSO - replicate 3

description:
BT89_DMSO_3
BT89_DMSO_CB839_processed.txt

value: DMSO


title: 8858-1_3_572

description: cortical organoid

value: M

tag: iPSc line

tag: differentiation


title: 1205-4_1_392

description: cortical organoid

tag: differentiation day

tag: batch


title: Rat 2_Thick Henle Loop_C

description: small RNA

value: Rat 2

value: Sprague Dawley

value: kidney

tag: age


title: Rat 1_Collecting Duct_D

description: small RNA

value: Collecting Duct


title: Rat 1_Proximal Tubule_D

description: small RNA

value: Proximal Tubule


title: 2242-1_NA_617

description: cortical organoid


title: BT89 treated with CB839 - replicate 1

description:
BT89_CB839_1
BT89_DMSO_CB839_processed.txt


title: BT89 treated with DMSO - replicate 2

description:
BT89_DMSO_2
BT89_DMSO_CB839_processed.txt


title: 0307-1_1_119

description: cortical organoid


title: BT89 treated with DMSO - replicate 1

description:
BT89_DMSO_1
BT89_DMSO_CB839_processed.txt


title: Rat 2_Collecting Duct_C

description: small RNA


title: KO-3

city: shanghai

first: xiaoxue

last: li

address: huashan road

institute: shanghai jiaotong university

data_processing:
Illumina sequencing with paired-ends 2x150 as the sequencing mode
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 software
Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie
To annotate genes with gene ontology (GO) terms, ClusterProfiler (R package) was used
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file including RPKM values for each Sample

source_name: skin

extract_protocol:
skin were isolated from Setd2fl/fl and Setd2K5-KO mice . Each sample contained 3 independent repeated animals
NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) was used for the construction of sequencing libraries.

tag: genotype


title: BT67 treated with CB839 - replicate 2

description:
BT67_CB839_2
BT67_DMSO_CB839_processed.txt


title: Rat 3_Proximal Tubule_C

description: small RNA

tag: tissue


title: 1205-4_1_70

description: cortical organoid

tag: Sex


title: 1205-4_12_183

description: cortical organoid


title: 1205-4_12_70

description: cortical organoid


title: 0307-1_1_126

description: cortical organoid


title: KO-1


title: Rat 3_Collecting Duct_C

description: small RNA


title: WT-2


title: BT67 treated with CB839 - replicate 1

description:
BT67_CB839_1
BT67_DMSO_CB839_processed.txt


title: BT67 treated with DMSO - replicate 3

description:
BT67_DMSO_3
BT67_DMSO_CB839_processed.txt


title: WT-3


title: WT-1


title: BT67 treated with CB839 - replicate 3

description:
BT67_CB839_3
BT67_DMSO_CB839_processed.txt


title: Rat 3_Thick Henle Loop_C

description: small RNA

value: Thick Henle Loop


title: 1205-4_1_419

description: cortical organoid


title: input-WT

data_processing:
Illumina NextSeq 500 used for sequencing
The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 (v2.2.6) software
Peak detection was performed using the MACS (v2.1.1)  peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file obtained by annotating the peak with the ChIPseeker package in the original file WT_peaks.narrowPeak.chr.xlsx after MACS2 search.

source_name: skin primary keratinocytes

extract_protocol:
primary mouse keratinocytes were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti- H3K36me3 antibodies.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq 500 with single-end 1x75 as the sequencing mode.


title: BT67 treated with DMSO - replicate 2

description:
BT67_DMSO_2
BT67_DMSO_CB839_processed.txt


title: 8858-3_1_392

description: cortical organoid


title: Rat 1_Thick Henle Loop_C

description: small RNA


title: CD8TEM_O2

city: Xi’an

first: Anjun

last: Jiao

address: No. 28, Xianning West Road, Xi'an City, Shaanxi Province

institute: Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University

data_processing:
The BGISEQ-500 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the BGISEQ-500 platform (Beijing Genomics Institute, BGI) after pooling according to its expected data volume and effective concentration.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: effector memory CD8+ T cells

growth_protocol: ZsGreen+ CD4 TEM, CD4 TCM, CD4 naïve T cells, and CD8 TEM, CD8 TCM, and CD8 naïve T cells were sorted from the spleens of TCRδCreERR26ZsGreen mice at the age of 8 weeks (Young) and 78 weeks (Old), respectively.

extract_protocol:
Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control using the Agilent RNA 6000 Nano Kit with the Agilent 2100 Bio analyse (Agilent Technologies). Library construction and RNA sequencing on the BGISEQ-500 platform were conducted at the Beijing Genomics Institute (BGI).
RNA libraries were prepared for sequencing according to the standard protocols provided by the Beijing Genomics Institute (BGI).

treatment_protocol: For long-term tracing experiments, TCRδCreERR26ZsGreen mice (five weeks old, n= 10) were treated with three doses of 1 mg/mouse tamoxifen intraperitoneal injection (i.p.) every other day. For short-term tracing experiments, TCRδCreERR26ZsGreen mice (five weeks old, n = 8) were treated with one dose of tamoxifen (1 mg/mouse).

value: TCR{delta}CreERR26ZsGreen mice

value: spleen

value: effector memory CD8+ T cells from the spleens of young mice (78 wks)


title: CD8TEM_O1


title: CD8TEM_Y2

value: effector memory CD8+ T cells from the spleens of young mice (8 wks)


title: BT67 treated with DMSO - replicate 1

description:
BT67_DMSO_1
BT67_DMSO_CB839_processed.txt

value: Brain tumor stem cell