title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019517_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018507_G1]

status: Public on Mar 19 2021

type: genomic

city: Memphis

first: Zhaoming

last: Wang

state: TN

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

country: USA

institute: St. Jude Children's Research Hospital

description: blood from survivor of childhood cancer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChips using standard Illumina protocal

scan_protocol: Arrays were stained and scanned using the Illumina HiScan system with standard recommended Illumina scanner setting

data_processing:
GenomeStudio V2011.1
Unmethylated and methylated signal intensities provided in the SJLIFE_IlluminaEPIC_2052samples_GEO_03162021_signal.txt
Average Beta provided in the SJLIFE_IlluminaEPIC_2052samples_GEO_03162021_processed.txt

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Standard Illumina Protocal

extract_protocol: DNA extracted from periperihal blood mononuclear cells using the QIAamp DNA Blood Mini Kit (Qiagen cat#51106)

tag: gender

value: Female

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: ASGr14

type: SRA

city: New Haven

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

institute: Yale University

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
ASGr14_TACATCGG

library_source: transcriptomic

data_processing:
fastq files were aligned to the WS274 genome using STAR on default settings, and duplicate reads were removed using samtools markup
BAM files resulting from the alignments were summarized to genes using the featureCounts tool
Genome_build: WS274
Supplementary_files_format_and_content: tab-delimited text file includes raw counts from featureCounts

molecule: total RNA

organism: Caenorhabditis elegans

source_name: FACS C. elegans neurons

growth_protocol:
Worms were grown on 8P nutrient agar 150 mm plates seeded with E. coli strain NA22
Sorting protocol: Fluorescence Activated Cell Sorting (FACS) was performed on a BD FACSAria™ III equipped with a 70-micron diameter nozzle. Cells were sorted into Trizol reagent LS

extract_protocol:
RNA was isolated using chloroform extraction
Libraries were prepared using Tecan SoLo Ovation RNAseq library

tag: tissue/cell type

value: FACS isolated ASG Neurons

tag: treatment

value: untreated


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019329_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018418_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST018641_G1]

description: blood from survivor of childhood cancer

value: Male


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019168_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019123_G1]

description: blood from survivor of childhood cancer


title: AVEr40

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AVEr40_CCGGAATA

value: FACS isolated AVE Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019645_G1]

description: blood from survivor of childhood cancer


title: ASGr15

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
ASGr15_ATCGTCTC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001218_G1]

description: blood from survivor of childhood cancer


title: ASGr13

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
ASGr13_CGACCTAA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019408_G1]

description: blood from survivor of childhood cancer


title: AVEr41

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AVEr41_CCAAGTAG


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019428_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018939_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019247_G1]

description: blood from survivor of childhood cancer


title: SAM24348281 Young 2 Midgut ISCs Intestine Small SAM24348281 Young 2 Midgut ISCs Young

city: Warsaw

first: Michal

last: Pawlak

address: Domaniewska 39 B

country: Poland

institute: Roche Polska Sp. z o.o.

description: Transcriptome profiling of Drosophila intestinal stem cells (ISCs) in the aging.

data_processing: Reads were aligned to the BDGP6 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were based on Refseq canonical transcripts mapped to BDGP6. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

organism: Drosophila melanogaster

source_name: intestinal stem cells

extract_protocol: For RNA-seq, between 62,000 - 210,000 ISCs were sorted directly into Buffer RLT and RNA was isolated using the RNeasy Mikro Kit (Qiagen). QC of samples was done to determine RNA quantity and quality prior to the processing by low input RNA-seq method. The concentration of 25 RNA samples was measured using DS-11 spectrophotometer (DeNovix) and the integrity of RNA was determined by 2100 Bioanalyzer (Agilent Technologies). Approximately few ng of total RNA was used as an input material for the library generation using SMART-seq v4 Ultra Low Input RNA kit (Clontech). Size of the libraries was confirmed using 4200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq4000 (Illumina) to generate >30M of single end 50 base pair reads.

tag: samid

value: Young 2 Midgut ISCs

value: Intestine Small

value: SAM24348281 Young 2 Midgut ISCs

value: Young


title: SAM24348284 Mid-age 1 Midgut ISCs Intestine Small SAM24348284 Mid-age 1 Midgut ISCs MidAge

value: Mid-age 1 Midgut ISCs

value: SAM24348284 Mid-age 1 Midgut ISCs

value: MidAge


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL018757_G1]

description: blood from survivor of childhood cancer


title: SAM24348283 Young 4 Midgut ISCs Intestine Small SAM24348283 Young 4 Midgut ISCs Young

value: Young 4 Midgut ISCs

value: SAM24348283 Young 4 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018862_G1]

description: blood from survivor of childhood cancer


title: SAM24348282 Young 3 Midgut ISCs Intestine Small SAM24348282 Young 3 Midgut ISCs Young

value: Young 3 Midgut ISCs

value: SAM24348282 Young 3 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019186_G1]

description: blood from survivor of childhood cancer


title: SAM24348390 Young 6 Midgut ISCs  Intestine Small SAM24348390 Young 6 Midgut ISCs  Young

value: Young 6 Midgut ISCs

value: SAM24348390 Young 6 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019135_G1]

description: blood from survivor of childhood cancer


title: SAM24348286 Mid-age 3 Midgut ISCs Intestine Small SAM24348286 Mid-age 3 Midgut ISCs MidAge

value: Mid-age 3 Midgut ISCs

value: SAM24348286 Mid-age 3 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS019206_G1]

description: blood from survivor of childhood cancer

value: Female


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018963_G1]

description: blood from survivor of childhood cancer


title: SAM24348289 Old 3 Midgut ISCs Intestine Small SAM24348289 Old 3 Midgut ISCs Old

value: Old 3 Midgut ISCs

value: SAM24348289 Old 3 Midgut ISCs

value: Old


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018934_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019509_G1]

description: blood from survivor of childhood cancer


title: SAM24348389 Young 5 Midgut ISCs  Intestine Small SAM24348389 Young 5 Midgut ISCs  Young

value: Young 5 Midgut ISCs

value: Intestine Small

value: SAM24348389 Young 5 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018699_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019180_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL019375_G1]

description: blood from survivor of childhood cancer

value: Male


title: SAM24348387 Very old 2 Midgut ISCs_76-78d Intestine Small SAM24348387 Very old 2 Midgut ISCs_76-78d VeryOld

value: Very old 2 Midgut ISCs_76-78d

value: VeryOld


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB003947_G2]

description: blood from survivor of childhood cancer


title: SAM24348288 Old 2 Midgut ISCs Intestine Small SAM24348288 Old 2 Midgut ISCs Old

value: Old 2 Midgut ISCs

value: SAM24348288 Old 2 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML019105_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018893_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018948_G1]

description: blood from survivor of childhood cancer


title: SAM24348386 Very old 1 Midgut ISCs_73-76d Intestine Small SAM24348386 Very old 1 Midgut ISCs_73-76d VeryOld

value: Very old 1 Midgut ISCs_73-76d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019652_G1]

description: blood from survivor of childhood cancer


title: SAM24348287 Old 1 Midgut ISCs Intestine Small SAM24348287 Old 1 Midgut ISCs Old

value: Old 1 Midgut ISCs

value: SAM24348287 Old 1 Midgut ISCs


title: SAM24348280 Young 1 Midgut ISCs Intestine Small SAM24348280 Young 1 Midgut ISCs Young

value: Young 1 Midgut ISCs

value: SAM24348280 Young 1 Midgut ISCs

value: Young


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019654_G1]

description: blood from survivor of childhood cancer

value: Female


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019009_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019637_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018777_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019497_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018620_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018607_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018590_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018902_G1]

description: blood from survivor of childhood cancer


title: SAM24348285 Mid-age 2 Midgut ISCs Intestine Small SAM24348285 Mid-age 2 Midgut ISCs MidAge

value: Mid-age 2 Midgut ISCs

value: SAM24348285 Mid-age 2 Midgut ISCs

value: MidAge


title: SAM24348388 Very old 3 Midgut ISCs_70d Intestine Small SAM24348388 Very old 3 Midgut ISCs_70d VeryOld

value: Very old 3 Midgut ISCs_70d

value: Intestine Small

value: SAM24348388 Very old 3 Midgut ISCs_70d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019466_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019583_G1]

description: blood from survivor of childhood cancer

value: Male


title: SAM24348391 Young 7 Midgut ISCs  Intestine Small SAM24348391 Young 7 Midgut ISCs  Young

value: Young 7 Midgut ISCs

value: SAM24348391 Young 7 Midgut ISCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018775_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018657_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB018847_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL018753_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018780_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018829_G1]

description: blood from survivor of childhood cancer


title: SAM24366246 1. ISCts_PcRNAi_36070_ 6.17.2019_10d Intestine Small SAM24366246 1. ISCts_PcRNAi_36070_ 6.17.2019_10d B1

description: Transcriptome profiling of Drosophila intestinal stem cells (ISCs) after Polycomb (Pc) knockdown.

tag: sampleID

tag: batch


title: SAM24366248 3. ISCts_PcRNAi_36070_ 6.26.2019_9d Intestine Small SAM24366248 3. ISCts_PcRNAi_36070_ 6.26.2019_9d B3


title: SAM24366243 1. ISCts_CherryRNAi 6.17.2019_10d Intestine Small SAM24366243 1. ISCts_CherryRNAi 6.17.2019_10d B1

value: 1. ISCts_CherryRNAi 6.17.2019_10d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018650_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018583_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019751_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018892_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes


title: SAM24366247 2. ISCts_PcRNAi_36070_ 6.20.2019_10d Intestine Small SAM24366247 2. ISCts_PcRNAi_36070_ 6.20.2019_10d B2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018899_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt


title: SAM24366245 3. ISCts_CherryRNAi 6.26.2019_9d Intestine Small SAM24366245 3. ISCts_CherryRNAi 6.26.2019_9d B3

value: 3. ISCts_CherryRNAi 6.26.2019_9d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019519_G1]

description: blood from survivor of childhood cancer

tag: chestrt

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018670_G1]

description: blood from survivor of childhood cancer

tag: pelvicrt


title: ISC PcRNAi rep3

library_source: genomic

data_processing:
Briefly, reads shorter than 18 bp were filtered out and GSNAP (version 2013-11-102) was used to map the reads to the BDGP6 reference genome. Duplicated reads have been were marked with Picard (2.23) and bam files belonging to the same group were merged using bamtools (2.3.0). MACS2 (2.1.0) with parameters (--pvalue 0.01, --shift -100, --extsize 199) was used to call the peaks. Highly reproducible peaks from replicates were assigned by the Irreproducibility Discovery Rate (IDR) ENCODE framework. Reads within overlapping peaks were counted by using the summarizeOverlaps method from the GenomicAlignments (1.18.1) R package. Counts were normalized using the TMM method, and then transformed using the voom method.
Genome_build: BDGP6
Supplementary_files_format_and_content: Tables of peaks with genomic corrdinates, annotations, significance in each condition and counts in each replicate

extract_protocol:
For ATAC-seq analysis, the protocol described in (Buenrostro, Wu, Chang, & Greenleaf, 2015) was used with minor adjustments. For each ATAC-seq sample, 100,000 YFP+ ISCs were sorted by FACS and cells were immediately spun down at 4  ̊C, washed, and then lysed and released nuclei were used in a transposition reaction using Nextera DNA Sample prep kit according to manufacturer’s protocol (Illumina). Transposed DNA was purified using MiniElute Reaction Cleanup kit (Qiagen) and eluted in 10 μl water. Purified transposed samples were amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) per manufacturer’s user guide.
Generated libraries were quantified by qPCR to determine the cycle number at which each sample produced 25% of maximum fluorescent intensity. The fluorescent intensity was used to estimate the number of additional PCR cycles required for each sample. Libraries were purified using SPRIselect beads (Beckman Coulter) to remove contaminating primer dimers. Library quality was assessed with dsDNA HS Assay kit (Thermo Fisher) and quantitated by Qubit 3.0 Fluorometer (Thermo Fisher). Pooled libraries were quantitated by Kapa Library Quantification Kit (Kapa Biosystems) and sequenced on Illumina HiSeq2500 to generate 30 M of pair end 50 bp reads per library.

tag: treatment

value: PcRNAi


title: SAM24366244 2. ISCts_CherryRNAi 6.20.2019_10d Intestine Small SAM24366244 2. ISCts_CherryRNAi 6.20.2019_10d B2

value: 2. ISCts_CherryRNAi 6.20.2019_10d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018879_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018687_G1]

description: blood from survivor of childhood cancer


title: ISC cherryRNAi rep3

tag: samid

value: cherryRNAi


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018530_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019734_G1]

description: blood from survivor of childhood cancer


title: ISC PcRNAi rep2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018707_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018516_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019614_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST018643_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019760_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019739_G1]

description: blood from survivor of childhood cancer


title: ISC very old rep3 [ATAC-Seq]

value: VeryOld


title: ISC PcRNAi rep1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018673_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018870_G1]

description: blood from survivor of childhood cancer


title: ISC very old rep2 [ATAC-Seq]


title: ISC very old rep1 [ATAC-Seq]


title: ISC young rep7 [ATAC-Seq]

value: Young


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB018840_G1]

description: blood from survivor of childhood cancer

value: Female


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018766_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018877_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017887_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019580_G1]

description: blood from survivor of childhood cancer


title: ISC young rep6 [ATAC-Seq]


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019405_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018438_G1]

description: blood from survivor of childhood cancer


title: ISC young rep5 [ATAC-Seq]


title: ISC cherryRNAi rep2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004739_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018618_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019668_G1]

description: blood from survivor of childhood cancer


title: ISC cherryRNAi rep1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019034_G1]

description: blood from survivor of childhood cancer


title: ISC old rep3 [ATAC-Seq]

value: Old


title: ISC old rep2 [ATAC-Seq]


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL019799_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018679_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019321_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017931_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018439_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018596_G1]

description: blood from survivor of childhood cancer


title: Alkbh8Def ID 547 APAP

city: Albany

first: Thomas

last: Begley

address: 1400 Washington Ave

institute: SUNY Albany

data_processing:
Windows terminal bash scripting to align back to genome
Sorted by coordinate gene count files for each sample
Data matrix of differential gene expression
Genome_build: mm9
Supplementary_files_format_and_content: csv files were generated using R Studio differential experession library for various reported comparison conditions

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Male C57BL/6 mice were 8-12 weeks of age.

extract_protocol:
Total RNA was isolated from liver tissue. Samples were placed in 1 mL of Trizol reagent (Invitrogen, CA), then homogenized with a Tissue-Tearor homogenizer (BioSpec, Bartlesville, OK). RNA isolation was performed using manufacturer’s protocol (catalog no. 15596026, Thermo Fisher Scientific). Isolated RNA samples were treated with DNase I, RNase-free (1 U/µL) (catalog no. EN0521, Thermo Scientific) following manufacturer’s instruction. Samples were then processed at The Center of Functional Genomics-University at Albany.
Libraries were prepared using Illumnia TruSeq Stranded mRNA using manufacturer's instruction.  Samples were sequenced using Illumina Nextseq500 Platform at 75 million single-end reads per run.

treatment_protocol: Either saline vehicle control or 600 mg/kg of acetaminophen was adminstered through intraperitoneal injection (I.P.).

tag: strain

tag: Sex

value: male

tag: genotype

value: Intraperitoneal injection:APAP

tag: tissue

value: liver

tag: group

value: acute


title: ISC mid age rep3 [ATAC-Seq]

tag: age


title: ISC old rep1 [ATAC-Seq]


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018953_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: ISC mid age rep2 [ATAC-Seq]


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018479_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites


title: Wildtype ID 530 APAP

value: wildtype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018565_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS017934_G1]

description: blood from survivor of childhood cancer


title: ISC mid age rep1 [ATAC-Seq]

tag: samid


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019750_G1]

description: blood from survivor of childhood cancer


title: Wildtype ID 525 APAP

tag: strain

tag: Sex

tag: genotype

tag: treatment


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018875_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age


title: ISC young rep4 [ATAC-Seq]


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018405_G1]

description: blood from survivor of childhood cancer

value: Male

tag: anthracyclines

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018935_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT019237_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes


title: Alkbh8Def ID 551 Saline

value: Intraperitoneal injection:Saline

tag: tissue

tag: group


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017959_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt

tag: chestrt

tag: abdominalrt


title: Alkbh8Def ID 550 Saline

tag: strain

tag: Sex


title: ISC young rep2 [ATAC-Seq]

tag: samid


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS010133_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: pelvicrt


title: ISC young rep3 [ATAC-Seq]

tag: age


title: Alkbh8Def ID 546 APAP

tag: genotype

tag: treatment


title: Alkbh8Def ID 549 Saline


title: ISC young rep1 [ATAC-Seq]


title: Alkbh8Def ID 545 APAP


title: Wildtype ID 526 Saline


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018574_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018584_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018473_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018433_G1]

description: blood from survivor of childhood cancer

tag: chestrt

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018622_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018648_G1]

description: blood from survivor of childhood cancer


title: Wildtype ID 521 Saline

tag: strain

tag: Sex

tag: tissue

tag: group


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018826_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019623_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018409_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017958_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: Wildtype ID 522 Saline

tag: genotype

tag: treatment


title: Alkbh8Def ID 588 APAP

value: chronic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018498_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vinca alkaloids

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT019231_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML018554_G1]

description: blood from survivor of childhood cancer

tag: abdominalrt


title: Alkbh8Def ID 587 APAP

tag: strain

tag: Sex

tag: tissue


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019598_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age


title: Wildtype ID 31 APAP

tag: group


title: Wildtype ID 32 APAP


title: Wildtype ID 30 APAP


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017924_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018869_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: shctrl_2

city: Hefei

first: Guang

last: Zhang

state: Anhui

address: 443 Huangshan Road, Shushan District

department: School of Basic Medical Sciences, Division of Life Sciences and Medicine

country: China

institute: university of science and technology of China

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg38
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

growth_protocol: A549 cell line was cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Sigma) supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: A549 cells were infected with shctrl or shUSP2-AS1 lentiviruses.

tag: cell line

tag: cell type

value: epithelial

tag: treatment

value: shctrl


title: shUSP2-AS1_1


title: Alkbh8Def ID 32 Saline

tag: genotype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018598_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: shUSP2-AS1_2


title: Alkbh8Def ID 589 APAP

tag: strain

tag: Sex

tag: tissue


title: shctrl_1


title: POINTseq_HCT116_CPSF73_KD_PlaB_Rep1

city: Lisboa

first: Rui

last: Sousa-Luís

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

data_processing:
Library strategy: POINT-5
POINT-seq and POINT-5 read adaptors were trimmed using TrimGalore v0.4.4 in paired-end mode, removing reads with less than 10 bases and/or low-quality ends (20 Phred score cut-off). The resultant reads were aligned against the reference human genome (GRCh38) using STAR v2.7.0 software (Dobin et al., 2013), requiring uniquely mapped reads (--outFilterMultimapNmax 1) and minimum alignment score (--outFilterScoreMin) of 10. Additionally, for POINT-5 the 5’end of the original RNA and their directionality was extracted. To do this, the script created for mNET-seq (Nojima et al., 2015) to obtain single nucleotide resolution profiles was adapted to define the 5’end of the first read in each pair as well as its directionality.
BAM files were split by strand with SAMtools v1.9 according their bitwise flags. In POINT-seq data, forward oriented strand had 83 and 163 flags associated while reverse oriented strand had 99 and 147 flags associated. Oppositely, 99 and 147 flags for POINT-5 correspond to the forward strand, while 83 and 163 to the reverse strand. For POINT-nano, 0 and 16 flags were used to call forward and reverse strand reads, respectively. Data was visualized applying genomeCoverageBed function of BedTools to each strand independently. Trackhubs in the UCSC browser were created by employing the UCSC bedGraphToBigWig v4 tool (Kent et al., 2002).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig format - read counts per bp for each strand
Supplementary_files_format_and_content: bigBed format - long reads split by strand

source_name: HCT116 CPSF73-AID cell

extract_protocol:
POINT method was performed as previously described mNET-seq protocol (Nojima et al., 2016) with some alterations.  In brief, crude nuclear fraction was prepared from HeLa or HCT116 cells (1x107 for POINT-seq and POINT-5, 4x107 for POINT-nano) as in mNET protocol. Chromatin pellet was resuspended in NUN1 (20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA and 50% Glycerol) and treated with modified NUN2 buffer (20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% NP-40, 1 M Urea, 3% Empigen, 1x proteasome inhibitor Complete (-EDTA) and 1x PhosSTOP). Note Empigen-treated nuclear solution was gently mixed by inverting tube a few times to avoid chromatin aggregation and incubated on ice for 10 min. The chromatin pellet was centrifuged at 400g for 30 sec. The pellet was washed with PBS twice and then digested in DNase solution (10 mM Tris-HCl (pH 7.5), 400 mM NaCl, 100 mM MnCl2, 2 U/mL RiboLock and 0.2 U/mL Turbo DNase) for 15 min. After DNA digestion, soluble digested chromatin was collected by 13,000 rpm centrifugation for 10 min. The supernatant was ten times-diluted in ice-cold NET-2E buffer (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 0.05 % NP-40 and 3% Empigen BB) and Pol II antibody-conjugated beads were added. 10 or 40 mg of Pol II antibody (200 or 800 mL of Dynabeads anti-mouse IgG) was used for POINT-seq and POINT-5 or POINT-nano methods. Immunoprecipitation was performed at 4oC for 1 hr. The beads were washed with 1 ml of ice-cold NET-2E buffer six times. The isolated nascent RNA was purified using Trizol reagent technology twice with once DNase treatment. Note that polyA tails were added to the isolated RNA by in vitro polyadenylation with E.coli PAP for POINT-nano. Then the pA+RNA was size-selected using SPRISelect reagent (x0.6 volume).
Library prep for illumina sequencing (NovaSeq6000) employed NEBNext Ultra II Directional RNA library prep kit and SMARTer Stranded RNA-seq kit for POINT-seq and POINT-5 analyses, respectively.  For ONT sequencing, Direct cDNA library prep kit was used for POINT-nano analysis. Illumina and ONT sequencing (PromethION) were conducted by Novogene UK and the high throughput genomics team of the Wellcome Trust Centre for Human Genetics (WTCHG), Oxford.

value: HCT116 CPSF73-AID cell


title: Alkbh8Def ID 31 Saline

tag: group


title: POINTseq_HCT116_CPSF73_Ctrl_PlaB_Rep2


title: POINTseq_HCT116_CPSF73_KD_PlaB_Rep2


title: Alkbh8Def ID 30 Saline


title: POINTseq_HCT116_CPSF73_Ctrl_DMSO_Rep2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018469_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: anthracyclines

tag: chestrt

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017927_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic

tag: corticosteroids

tag: pelvicrt


title: POINTseq_HCT116_CPSF73_Ctrl_PlaB_Rep1

tag: cell line

tag: treatment


title: POINTseq_HCT116_CPSF73_KD_DMSO_Rep2


title: Wildtype ID 32 Saline

tag: genotype


title: Wildtype ID 31 Saline


title: POINTseq_HCT116_CPSF73_Ctrl_DMSO_Rep1


title: POINTseq_HCT116_CPSF73_KD_DMSO_Rep1


title: Wildtype ID 30 Saline


title: POINT5_HCT116_Xrn2_KD_PlaB_Rep2

source_name: HCT116 Xrn2-AID cell

value: HCT116 Xrn2-AID cell


title: Wildtype ID 529 APAP


title: NC ctrl 72h 5

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

country: Germany

institute: Technical University of Munich

data_processing:
Sequencing on the Illumina NextSeq 500 platform with custom primer and High Output v2 kit (75 cycles) (Illumina, #FC-404-2005), Reads from barcoded mRNA-seq experiments have two barcodes, corresponding to the two levels of multiplexing. The first one is common to standard protocols and is used to separate the libraries. The second is specific to the barcoded mRNA-seq protocol and is used to separate the multiplexed samples from the bulk data.
The first demultiplexing step was performed with the Illumina BaseSpace platform, while the second was performed using custom scripts. FastQ files containing 62 bp long reads were analysed.
Sequenced reads were mapped to the murine genome, NCBI build 38, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM).
Genome_build: murine NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

source_name: primary brite adipocytes

growth_protocol: Primary preadipocytes were prepared from stromal-vascular fraction of murine inguinal white adipose tissue of 129SvEv mice, induced at sub-confluence for 2 days and differentiated for 1 day in the presence of rosiglitazone to induce browning.

extract_protocol:
Differentiating brite adipocytes were washed with PBS and scraped into Trisure (Bioline). Total RNA was prepared from Trisure (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were prepared from total RNA by tagmentation of full-length ds cDNA (5 ng) with Tn5 enzyme (1 µl, 11 µM) and amplified (15 cycles). AMPure beads (Beckman Coulter, #A63881) were used to size-select fragments of 200-1000 bp in two rounds (0.5x beads and 0.7x beads, respectively). Libraries were profiled with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-474), measured with the Qubit dsDNA HS Assay Kit (Invitrogen, #Q32851), pooled and sequenced on the Illumina NextSeq 500 platform with custom primer and High Output v2 kit (75 cycles) (Illumina, #FC-404-2005).

treatment_protocol: Cells were reverse transfected with lncRNA Ctcflos-targeting or non-targeting control LNA Gapmer Antisense oligonucleotides [50nM] and harvested either 24 hours or 72 hours post transfection.

tag: source organ

value: inguinal WAT


title: NC ctrl 72h 6


title: POINT5_HCT116_Xrn2_Ctrl_DMSO_Rep1


title: POINT5_HCT116_Xrn2_KD_DMSO_Rep2


title: NC ctrl 72h 4


title: POINT5_HCT116_Xrn2_KD_DMSO_Rep1


title: POINT5_HCT116_Xrn2_Ctrl_DMSO_Rep2


title: POINT5_HCT116_Xrn2_Ctrl_PlaB_Rep2


title: POINTseq_HCT116_Xrn2_KD_PlaB_Rep2


title: NC ctrl 72h 3


title: POINT5_HCT116_Xrn2_KD_PlaB_Rep1


title: POINTseq_HCT116_Xrn2_Ctrl_PlaB_Rep1


title: POINTseq_HCT116_Xrn2_KD_PlaB_Rep1


title: POINTseq_HCT116_Xrn2_Ctrl_PlaB_Rep2


title: POINTseq_HCT116_Xrn2_KD_DMSO_Rep2


title: NC ctrl 72h 1


title: Ctcflos KD 72h 6


title: NC ctrl 72h 2


title: POINTseq_HCT116_Xrn2_Ctrl_DMSO_Rep2


title: POINTseq_HCT116_Xrn2_KD_DMSO_Rep1


title: Ctcflos KD 72h 5


title: Ctcflos KD 72h 4


title: POINTseq_HCT116_CPSF73_KD_3hr_Rep1

value: IAA+


title: POINTseq_HCT116_Xrn2_Ctrl_DMSO_Rep1


title: POINTseq_HCT116_CPSF73_Ctrl_Rep2

value: IAA-


title: POINT5_HCT116_Xrn2_Ctrl_PlaB_Rep1


title: POINTseq_HCT116_Xrn2_KD_4hr_Rep2

value: IAA +


title: POINTseq_HCT116_CPSF73_Ctrl_Rep1

value: IAA -


title: POINTseq_HCT116_CPSF73_KD_3hr_Rep2


title: POINTseq_HCT116_Xrn2_Ctrl_Rep2


title: Ctcflos KD 72h 3


title: NC ctrl 24h 5


title: Ctcflos KD 72h 1


title: NC ctrl 24h 6


title: POINT5_HCT116_CPSF73_Ctrl_Rep2


title: POINT5_HCT116_CPSF73_Ctrl_Rep1


title: NC ctrl 24h 4


title: Ctcflos KD 72h 2


title: POINT5_HCT116_CPSF73_KD_3hr_Rep2


title: POINTseq_HCT116_Xrn2_Ctrl_Rep1


title: POINT5_HCT116_Xrn2_KD_4hr_Rep2


title: POINT5_HCT116_Xrn2_Ctrl_Rep2


title: POINT5_HCT116_Xrn2_KD_4hr_Rep1


title: POINT5_HCT116_Xrn2_Ctrl_Rep1


title: POINT5_HCT116_+ExT_Rep2


title: POINT5_HCT116_-ExT_Rep2


title: NC ctrl 24h 2


title: POINTseq_HCT116_Xrn2_KD_4hr_Rep1


title: NC ctrl 24h 3


title: POINT5_HCT116_+ExT_Rep1


title: POINT5_HCT116_CPSF73_KD_3hr_Rep1


title: Ctcflos KD 24h 6


title: POINT5_HCT116_-ExT_Rep1


title: Ctcflos KD 24h 5


title: Ctcflos KD 24h 4


title: Control_siRNA_1_control

data_processing:
Read preprocessing, alignment and counting was performed by HTSeqGenie (4.12.0). Reads were aligned against the reference Drosophila genome (BDGP6), using gene models based on the Flybase Drosophila melanogaster Annotation Set (v6.02). Reads falling within coding sequences were counted to determine an estimate of gene expression.
Genome_build: BDGP6

source_name: Control_siRNA_1, control

extract_protocol: For RNA-seq, between 62,000 – 210,000 ISCs were sorted directly into Buffer RLT and RNA was isolated using the RNeasy Mikro Kit (Qiagen). QC of samples was done to determine RNA quantity and quality prior to the processing by low input RNA-seq method. The concentration of RNA samples was measured using DS-11 spectrophotometer (DeNovix) and the integrity of RNA was determined by 2100 Bioanalyzer (Agilent Technologies). Approximately few ng of total RNA was used as an input material for the library generation using SMART-seq v4 Ultra Low Input RNA kit (Clontech).

tag: cell type

value: intestinal stem cells

value: control


title: SIRPα-KO M1 macrophage + mCD47.ex

city: Atlanta

first: Lei

last: Shi

state: GA

address: 100 Piedmont Avenue SE

department: Department of Biology

institute: Center for Diagnostics & Therapeutics

description: SIRPα-/-

data_processing:
Basecalls performed using Zebracall process version 0.5.0.13875
In order to decrease noise of sequencing data, data filtering was done firstly, which included: (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio is more than 50%; (3) Removing reads whose unknown base ('N' base) ratio is more than 10%. Then, all clean readswere  mapped to mm9 whole genome.
The fragment counts of each gene were normalized by fragments per kb per million (FPKM).
RNA-seq data were analyzed using R version 3.3.3 and the R package DeSeq2 for differential gene expression, graphical representation, and statistical analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include FPKM values and GO information for each sample

source_name: macrophage

growth_protocol: Macrophages were derived from bone marrow cells (bone marrow derived macrophages, BMDM) with murine macrophage colony stimulating factor (M-CSF)-conditioned RPMI-1640 medium for 5 days.

extract_protocol:
After treatment,  M1 BMDM from 5 SIRPα-KO or 5 WT mice were mixed and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: BMDMs produced from WT and SIRPα-KO mice were treated with IFNγ(20ng/ml) plus LPS (100ng/ml) in the presence of mCD47.ex for 6h

tag: stain

value: SIRPalpha-/-

value: bone marrow-derived macrophages


title: myotube circRNA 3

type: RNA

city: Guangzhou

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

description: Gene expression after differentiation

hyb_protocol: Mouse circRNAs array hybridization was performed based on the standard protocols of Arraystar Mouse circRNA Array V2.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Scanner G2505C.

data_processing: The scanned images were analyzed with Agilent feature extraction software (version 11.0.1.1).

source_name: cell line C2C12,incubation in DMEM containing 2% horse serum

label_protocol: Samples labeling were performed based on the standard protocols of Arraystar Mouse circRNA Array V2.

extract_protocol: According to the TRIzol regent (Life Technologies, USA) manufacturer's instructions, total RNA was extracted from the mouse C2C12 myoblasts and myotubes.

treatment_protocol: The mouse myoblast cell line C2C12 was cultured in DMEM high glucose supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 μg/mL of streptomycin in 5% CO2 at 37°C. When the cells reached 80–90% confluence, they were differentiated by incubation in DMEM containing 2% horse serum.

tag: differentiation status

value: myotube


title: NC ctrl 24h 1


title: Control_siRNA_2_control

source_name: Control_siRNA_2, control


title: myoblast circRNA 3

description: Gene expression

source_name: cell line C2C12

value: myoblast


title: ISC old rep2

data_processing:
Single-cell RNA-seq data for three independent biological replicates were processed with cellranger count (Cell Ranger 3.0.2; 10x Genomics) using standard parameters and supplying a custom reference package based on Drosophila melanogaster reference genome BDGP6
Genome_build: BDGP6
Supplementary_files_format_and_content: barcodes.tsv.gz contains barcode file generated during processing of cellranger count, features.tsv.gz contains gene annotation, matrix.mtx.gz is a sparse matrix with counts (UMI), sce.RDS.gz is a SingleCellExperiment object containing gene counts and meta data.

extract_protocol:
Whole midguts were dissected in 1xPBS, 1% BSA and dissociated at RT using 0.5% Trypsin-EDTA solution. Midguts were agitated by vortexing every 30 min and dissociated cells were removed from the enzyme solution and placed on ice in 1xPBS, 1% BSA and 2%FBS every 30 min. Once the tissue was completely dissociated, cells were FACS sorted to ensure single cells were obtained after which cell viability was measured using a Vi-CELL analyzer to confirm >80% viability. The cells were then immediately applied to the 10XGenomics chromium platform.
Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v2 following manufacturer’s user guide (10x Genomics).

tag: samid

value: Old


title: Trx_siRNA_2_Trx-KD

source_name: Trx_siRNA_2, Trx-KD

value: Trx-KD


title: WT M1 macrophage + mCD47.ex

value: wild type


title: Ctcflos KD 24h 2


title: POINT5_HCT116_Xrn2_KD_4hr_-ExT_Rep2


title: POINT5_HCT116_Xrn2_KD_4hr_-ExT_Rep1


title: myoblast circRNA 2

description: Gene expression


title: Col FRI mRNA-seq (biorep #3)

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description:
Paired-end 75 base read mRNA-seq data from third biological replicate of early heart Col FRI embryos (two sequencing runs)
fri_eh3

data_processing:
Transcriptome analyses were as described (Hofmann et al., 2019) except that FLC isoform models based on aligned read coverage and consensus poly(A) sites were included in the Kallisto-based pseudo-alignments (Bray et al., 2016).
Genome_build: TAIR10
Supplementary_files_format_and_content: TSV files for mRNA-seq processed data files (SAMPLE.kallisto.tsv) were output from Kallisto (Bray et al. 2016) and have following four columns: 1) target_id, transcript isoform; 2) length, length of transcript isoform; 3) eff_length, effective length of transcript isoform; 4) est_counts, estimated counts based on pseudoalignment; 5) tpm, transcripts per million

organism: Arabidopsis thaliana

source_name: FRI_Early heart embryos

growth_protocol: Seeds were surface sterilized and stratified at 4° C for three days before sown on soil. Col FRI seeds (1) were initially grown on ½× MS media without sucrose for 7 days in long day-condition (21° C, 16h light/ 8h dark cycle) and transferred to 4° C under short-day conditions (8h light/16h dark cycle) for 6 weeks of vernalization prior to transferring the seedlings to the soil. All plants were grown in a climate-controlled growth chamber at 20° C to 22° C under a 16h light/8h dark cycle.

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific)
Smart-seq2 cDNA libraries were generated as described (Hofmann et al., 2019) with the following modifications. Twenty heart stage embryos were dissected from Col-0, Col FRI and, 35S::FCA genotypes and NGS libraries were prepared using non-commercial Tn5 for library tagmentation.

tag: accession

value: FRI

tag: tissue

value: Early heart embryos


title: myotube circRNA 1

description: Gene expression after differentiation


title: myotube circRNA 2

description: Gene expression after differentiation


title: ISC young rep2

tag: age

value: Young


title: Ctcflos KD 24h 1

value: inguinal WAT


title: Trx_siRNA_1_Trx-KD

source_name: Trx_siRNA_1, Trx-KD


title: Col FRI mRNA-seq (biorep #2)

description:
Paired-end 75 base read mRNA-seq data from second biological replicate of early heart Col FRI embryos (two sequencing runs)
fri_eh2


title: POINT5_HCT116_Xrn2_KD_Timepoint_4hrs

value: HCT116 Xrn2-AID cell

value: XRN2 KD Timepoint 4hrs


title: myoblast circRNA 1

description: Gene expression


title: ISC old rep1


title: Ctcflos KD 24h 3


title: POINT5_HCT116_Xrn2_KD_4hr_+ExT_Rep1


title: POINT5_HCT116_Xrn2_KD_Timepoint_2hrs

value: XRN2 KD Timepoint 2hrs


title: ISC young rep1


title: POINT5_HCT116_Xrn2_KD_Timepoint_1hrs

value: XRN2 KD Timepoint 1hrs


title: POINT5_HCT116_Xrn2_KD_Timepoint_0.5hrs

value: XRN2 KD Timepoint 0.5hrs


title: ISC mid age rep1


title: 35S::FCA mRNA-seq (biorep #2)

description:
Paired-end 75 base read mRNA-seq data from second biological replicate of early heart 35S::FCAembryos (two sequencing runs)
FCA_eh2

source_name: 35S::FCA_Early heart embryos


title: mASO Scrbl iExos-2

city: Houston

first: Raghu

last: Kalluri

address: 1881 East road

department: Cancer Biology

institute: MD Anderson Cancer Center

data_processing:
Liver RNA sequencing was performed using Illumina TrueSeq stranded mRNA seq
Genome mapping was performed using TopHat software
Cufflinks algorithm were used for identification of transcripts from RNA-Seq data and normalization of the expression value
Supplementary_files_format_and_content: abundance measurements; raw counts

source_name: mASO Scrbl iExos_liver

extract_protocol:
Total RNA was extracted from livers using TRIzol. RNA integrity was determined using RNA 6000 Nano Assay by the MDACC Sequencing and ncRNA Program core. Liver RNA sequencing was performed using Illumina TrueSeq stranded mRNAseq MDACC Sequencing and ncRNA Program core.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BALB/c

value: injection mASO Scrbl iExos as control

value: Liver


title: KO-mtb-4

city: Seoul

first: June-young

last: Lee

department: Dept. of Biology

country: South Korea

institute: KyungHee University

data_processing:
The base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38(mm10) whole genome using Salmon
Salmon quantification file was imported to Deseq2 and visualized.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-separated file with gene quantification file

source_name: Macrophage

extract_protocol:
Bone marrow derived macrophage was isolated using Trizol reagent and Purelink RNA mini kit. Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used and sequencing libraries preapred by TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E.
mRNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

value: Bone marrow derived macrophage

value: Mitofusion 2 knock out

value: Mycobacterium treatment


title: 35S::FCA mRNA-seq (biorep #1)

description:
Paired-end 75 base read mRNA-seq data from first biological replicate of early heart 35S::FCA embryos (two sequencing runs)
FCA_eh1


title: Col-0 mRNA-seq (biorep #3)

description:
Paired-end 75 base read mRNA-seq data from third biological replicate of early heart Col-0 embryos (two sequencing runs)
Col_eh3

source_name: wild type_Early heart embryos


title: mASO STAT3 iExos-3

source_name: mASO STAT3 iExos_liver

value: injection mASO STAT3 iExos as experimental group


title: mASO STAT3 iExos-2


title: KO-mtb-3


title: POINT5_HCT116_Xrn2_KD_4hr_+ExT_Rep2


title: KO-mtb-2


title: mASO STAT3 iExos-1


title: POINTseq_HCT116_Xrn2_KD_Timepoint_1hrs

data_processing:
Library strategy: POINT-seq
POINT-seq and POINT-5 read adaptors were trimmed using TrimGalore v0.4.4 in paired-end mode, removing reads with less than 10 bases and/or low-quality ends (20 Phred score cut-off). The resultant reads were aligned against the reference human genome (GRCh38) using STAR v2.7.0 software (Dobin et al., 2013), requiring uniquely mapped reads (--outFilterMultimapNmax 1) and minimum alignment score (--outFilterScoreMin) of 10. Additionally, for POINT-5 the 5’end of the original RNA and their directionality was extracted. To do this, the script created for mNET-seq (Nojima et al., 2015) to obtain single nucleotide resolution profiles was adapted to define the 5’end of the first read in each pair as well as its directionality.
BAM files were split by strand with SAMtools v1.9 according their bitwise flags. In POINT-seq data, forward oriented strand had 83 and 163 flags associated while reverse oriented strand had 99 and 147 flags associated. Oppositely, 99 and 147 flags for POINT-5 correspond to the forward strand, while 83 and 163 to the reverse strand. For POINT-nano, 0 and 16 flags were used to call forward and reverse strand reads, respectively. Data was visualized applying genomeCoverageBed function of BedTools to each strand independently. Trackhubs in the UCSC browser were created by employing the UCSC bedGraphToBigWig v4 tool (Kent et al., 2002).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig format - read counts per bp for each strand
Supplementary_files_format_and_content: bigBed format - long reads split by strand


title: KO-mtb-1


title: siSTAT3 iExos-3

source_name: siSTAT3 iExos_liver

value: injection siSTAT3 iExos as experimental group


title: 35S::FCA mRNA-seq (biorep #3)

description:
Paired-end 75 base read mRNA-seq data from third biological replicate of early heart 35S::FCA embryos (two sequencing runs)
FCA_eh3


title: POINTseq_HCT116_Xrn2_KD_Timepoint_2hrs


title: KO-unt-4

value: Untreated


title: siSTAT3 iExos-2


title: KO-unt-3


title: mASO Scrbl iExos-3


title: POINTseq_HCT116_Xrn2_KD_Timepoint_0.5hrs


title: KO-unt-2


title: POINTseq_HCT116_Xrn2_KD_Timepoint_0hrs

value: XRN2 KD Timepoint 0hrs


title: siCntrl iExos-3

source_name: siCntrl iExos_liver

value: injection siCntrl iExos as control


title: POINTseq_HCT116_Xrn2_KD_Timepoint_4hrs

source_name: HCT116 Xrn2-AID cell


title: siSTAT3 iExos-1


title: Col-0 mRNA-seq (biorep #2)

description:
Paired-end 75 base read mRNA-seq data from second biological replicate of early heart Col-0 embryos (two sequencing runs)
Col_eh2

value: wild type

value: Early heart embryos


title: siCntrl iExos-2


title: KO-unt-1


title: Col-0 mRNA-seq (biorep #1)

description:
Paired-end 75 base read mRNA-seq data from first biological replicate of early heart Col-0 embryos (two sequencing runs)
Col_eh1


title: POINTseq_HeLa_DRB_Ctrl_DMSO_Rep2

source_name: HeLa cell

value: HeLa

value: DMSO


title: WT-mtb-4

value: Wild type


title: SC Fa2N-4 (48 h), S18

city: Berlin

first: Florian

last: Padberg

address: Max-Dohrn-Strasse 8-10

department: Chemicals and Product Safety

institute: German Federal Institute for Risk Assessment (BfR)

hyb_protocol: Hybridization was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

scan_protocol: Array scanning was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) according to the manufacturer's instruction (Affymetrix).

data_processing:
Raw data were processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Further analysing was done using Transcriptome Analysis Console (TAC) Software 4.0.
RNA expression value derived from Expression Console software; core-exon analysis

label: biotin

label_protocol: Labelling was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

growth_protocol: Fa2N-4 cells were grown in Williams E (PAN-Biotech, Aidenbach, Germany) with supplements at 37 °C and 5 % CO2. Monocyte derived macrophages (MDM) were differentiated from human PBMCs. Monocytes were separated due to the adhesion-properties of the cells. Differentiation  was started using RPMI containing 10 % (v/v) FCS and 25 ng/ml macrophage-colony-stimulating factor (M-CSF) over six days with a medium change every two days. MDM were seeded either in the well directly (for the single-cultivation) or in the Falcon® cell culture inserts (VWR, Darmstadt, Germany) for the co-cultivation using Williams E medium. The 50% and the 15% MDM corresponded to a density of 1 x 10e5 and 0.3 x 10e5 cells per cm2, respectively.

extract_protocol: RNA was isolated using the NucleoSpin® RNA Kit (Machery-Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: Fa2N-4 cells were incubated with or without indirect contact to monocyte derived macrophages at different cell ratios for 24 h or 48 h.

value: SV-40 immortalized hepatic cell line (Fa2N-4)

value: Single-culture Fa2N-4

tag: time


title: POINTseq_HeLa_DRB_Rep1

value: DRB


title: POINT5_HCT116_Xrn2_KD_Timepoint_0hrs

value: HCT116 Xrn2-AID cell


title: POINTseq_HeLa_DRB_Rep2


title: POINTseq_HeLa_DRB_Ctrl_DMSO_Rep1


title: POINTseq_HeLa_PlaB_Rep2

value: PlaB


title: Cow: 4408 Trt: 0

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

data_processing:
Reads were mapped to the ENSEMBL bovine genome
EBseq analysis was utilized to identify differently expressed genes
Supplementary_files_format_and_content: Fastq files followed cow number_period_sample_replicate
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

organism: Bos taurus

source_name: Milk RNA

extract_protocol:
Milk samples were collected and centrifuged at 2,000 x g for 10 min to separate the milk fat. The milk fat was removed to a separate vial, an equal volume of RNAse free water and Trizol added. An equal volume of chloroform was added and the entire sample was centrifuged at 12,000 x g. After centrifuging 70% ethanol was added. RNA was cleaned by Qiagen RNAeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Holstein

tag: stage of lactation

value: Early Lactation

value: control

tag: sample type

value: milk


title: WT-mtb-3

value: Bone marrow derived macrophage

value: Mycobacterium treatment


title: siCntrl iExos-1

value: BALB/c

value: injection siCntrl iExos as control

value: Liver


title: WT-mtb-1


title: WT-mtb-2


title: POINTseq_HeLa_PlaB_Rep1

value: HeLa


title: Cow: 4394 Trt: 63

value: postruminal lysine treatment for 63 days


title: Cow: 4408 Trt: 63


title: WT-unt-4

value: Wild type

value: Untreated


title: Cow: 4394 Trt: 0


title: POINTseq_HeLa_DMSO_Rep1

value: DMSO


title: WT-unt-1


title: POINTseq_HeLa_Untr_Rep3


title: Cow: 4381 Trt: 63


title: WT-unt-2


title: SC Fa2N-4 (24 h), S15

value: SV-40 immortalized hepatic cell line (Fa2N-4)

value: Single-culture Fa2N-4


title: POINTseq_HeLa_Untr_Rep2


title: WT-unt-3


title: Cow: 4381 Trt: 0


title: aged HSC 12 hour

city: Minato-ku

first: Atsushi

last: Iwama

state: Tokyo

address: 4-6-1, Shirokanedai

department: Center for Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
alignment:TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser;) with annotation data from iGenomes (Illumina)
Row count for each gene symbol are generated by StringTie
Data normalization:DESeq2
DESeq2 were used to perform statistical analysis for differentially expressed genes
Genome_build: mm10

source_name: 20 month hematopoietic stem cells

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen)
Total RNA were subjected to reverse transcription and amplification with a SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). After sonication with an ultrasonicator (Covaris), the libraries for RNA-seq were generated from fragmented DNA with 8 cycles of amplification using a NEB Next Ultra DNA Library Prep Kit (New England BioLabs). After the libraries were quantified using the Bioanalyzer (Agilent), samples were subjected to sequencing with Hiseq1500 (Illumina) and 61 cycles of the sequencing reactions were performed.

treatment_protocol: Young and aged HSCs were stimulated with a mixture of cytokines (SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) (BioLegend) in S-Clone SF-O3 (Sanko Junyaku) supplemented with 10% FBS, 50 μM 2-ME, and 1% GPS

value: Murine bone marrow derived HSCs

tag: surface markers

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-

value: 12 hours after cytokine stimulation


title: POINTseq_HeLa_Untr_Rep1

tag: cell line


title: aged HSC 3 hour

tag: treatment

value: 3 hours after cytokine stimulation


title: CC 15% Fa2N-4 (24 h), S14

value: Co-culture 15% MDM Fa2N-4


title: CC 50% Fa2N-4 (24 h), S13

value: Co-culture 50% MDM Fa2N-4


title: CC 15% Fa2N-4 (48 h), S11


title: CC 50% Fa2N-4 (48 h), S16


title: CC 50% Fa2N-4 (24 h), S7


title: CC 50% Fa2N-4 (48 h), S10


title: CC 15% Fa2N-4 (48 h), S17


title: SC Fa2N-4 (48 h), S6


title: CC 15% Fa2N-4 (24 h), S8


title: SC Fa2N-4 (24 h), S9


title: Cow: 4345 Trt: 63

value: Holstein

value: Early Lactation

value: milk


title: aged HSC 0 hour

value: no cytokine stimulation


title: Cow: 4383 Trt: 0

value: control


title: POINT5_HeLa_Untr_Rep2

value: HeLa


title: Col FRI mRNA-seq (biorep #1)

description:
Paired-end 75 base read mRNA-seq data from first biological replicate of early heart Col FRI embryos (two sequencing runs)
fri_eh1

tag: genotype

value: FRI

value: Early heart embryos


title: POINT5_HeLa_Untr_Rep1

value: Untreated


title: Cow: 4383 Trt: 63

value: postruminal lysine treatment for 63 days


title: young HSC 12 hour

source_name: 10 week hematopoietic stem cells


title: POINTseq_HeLa_DMSO_Rep2

value: DMSO


title: Cow: 4319 Trt: 63


title: Cow: 4345 Trt: 0


title: 5hmC-Seal #2 on H1 WT hESCs

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

description:
5hmC-Seal
CHe-DW-59S-DH-2_S49

data_processing:
library strategy: 5hmC-Seal
FASTQ files were aligned using BWA 0.7.17.
5-hmC peak identification was performed using nonduplicate reads with Model-based Analysis of ChIP-Seq data (MACS14 1.4.2).
Genome_build: hg19
Supplementary_files_format_and_content: peak files in .txt format

source_name: 5hmC-Seal  on H1 WT hESCs

growth_protocol: H1 hESCs were maintained in the chemically defined feeder-free, serum-free E8 condition (Thermo Fisher Scientific, A1517001) on polystyrene plates coated with human recombinant vitronectin (Thermo Fisher Scientific, A14700) at 37°C with 5% CO2. hESCs were dissociated with 0.5 mM EDTA and split every 3–4 days at a 1:10–1:15 ratio. 10 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells were routinely confirmed to be mycoplasma-free by the MSKCC Antibody and Bioresource Core Facility. All experiments were approved by the Tri-SCI Embryonic Stem Cell Research Oversight Committee (ESCRO).

extract_protocol:
5hmC-Seal was performed on genomic DNA isolated from WT H1 hESCs. Briefly, 100 ng gDNA was fragmented, followed by A-tailing and ligation with sequencing adapters using the KAPA Hyper Prep Kit (KAPA Biosciences). Next, gDNA 5-hmC residues on fragments were subjected to T4 β-glucosyltransferase (Thermo) enzymatic modification with UDP-N3-glucose (Active Motif), followed by subsequent chemical modification with biotin-PEG4-dibenzocyclooctyne (DBCO, Sigma). Biotinylated gDNA fragments were separated using streptavidin M270 Dynabeads (Invitrogen) and PCR amplified.
Constructed sequencing libraries were purified with AMPure XP beads (Beckman Coulter), and paired-end sequencing was performed using the Illumina Novaseq 6000 sequencer.

treatment_protocol: No treatments were applied prior to genomic DNA extraction

value: H1 hESCs

value: human embryonic stem cells (hESCs)

value: Wild type sequence


title: young HSC 3 hour

value: Murine bone marrow derived HSCs

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-

value: 3 hours after cytokine stimulation


title: Cow: 4319 Trt: 0

value: Holstein


title: 5hmC-Seal #1 on H1 WT hESCs

description:
5hmC-Seal
CHe-DW-59S-DH-1_S48


title: mASO Scrbl iExos-1

value: BALB/c

value: injection mASO Scrbl iExos as control

value: Liver


title: 4.5 dpf CHT cells

status: Public on Mar 18 2021

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

description: CHT 4.5dpf  single cell RNA seq data

data_processing:
UMI-tools was used to analysis our single cell data.Firstly, in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI, and R2 is biological sequencing.
Then in “extract” step we filter some low-quality reads and non-UMI reads with recommend parameters, so that we can use STAR to map to the reference genome.
Finally, in “count” step we generate a gene expression matrix for following analysis.
Genome_build: GRCz10
Supplementary_files_format_and_content: Contains the expression level of all three samples, measured by UMI counts

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
Then single cell suspensions (300-1,000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10× Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 30 Library and Gel Bead Kit V2 (10× Genomics, 120237). Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads (Invitrogen, 37002D).
10X genomics scRNA-Seq: Single-cell RNA-sequencing (scRNA-seq) libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 (10× Genomics, 120237) following the manufacture’s introduction.

tag: genotype/variation

value: Tg (kdrl:mCherry/CD41:GFP)

value: 4.5 dpf

value: caudal hematopoietic tissue (CHT) region

value: endothelial cells+hematopoietic cells+ double negative niche cells


title: 3.5 dpf CHT cells

description: CHT 3.5dpf single cell RNA seq data

value: 3.5 dpf

tag: cell type


title: young HSC 0 hour

value: no cytokine stimulation


title: MtWT_4h_1

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 or Neurospora crassa FGSC 2489 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html) and Neurospora crassa OR74A genome (version 12)
Supplementary_files_format_and_content: tab-delimited text files including Reads count for each sample.

organism: Thermothelomyces thermophilus

source_name: the wild-type strain

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation. N. crassa strains were inoculated into 1×Vogel’s salt with 2% sucrose and grown for 16 h at 25 °C. Mycelia of the N. crassa were collected and washed with 1×Vogel’s salt several times, and transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type


title: Mtclr-4_4h_1


title: Mtclr-4_4h_2


title: MtWT_4h_2


title: S9901 H2

type: protein

city: Boston

first: Hui

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing: Normalization and interrun calibration were performed as described elsewhere (http://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf) In brief, correction for systematic effects on the data introduced during the hybridization step, median normalization within an array, and calibration between plates were performed.

molecule: protein

source_name: Primary beta-cells

extract_protocol: Primary beta-cells were culture in serum-free medium and used conditioned media were collected.

value: Primary beta-cells

tag: group

value: ABT


title: S6747 C4


title: S9901 A3

value: Momelotinib


title: S7453 D2


title: S6747 D4


title: S601 G3


title: S7453 B2


title: S4807 F1


title: CC 15% Fa2N-4 (48 h), S5

value: SV-40 immortalized hepatic cell line (Fa2N-4)

value: Co-culture 15% MDM Fa2N-4


title: SC Fa2N-4 (48 h), S12

value: Single-culture Fa2N-4


title: S9901 G2

value: Control


title: S601 F3


title: CC 50% Fa2N-4 (48 h), S4

value: Co-culture 50% MDM Fa2N-4


title: S6747 B4


title: S4807 D1


title: SC Fa2N-4 (24 h), S3


title: S601 E3


title: S4807 E1


title: S7453 A2


title: CC 15% Fa2N-4 (24 h), S2


title: CC 50% Fa2N-4 (24 h) , S1


title: S7453 G1


title: S6747 H3


title: S9901 E2


title: S601 B3


title: S4807 A1


title: S9901 F2


title: S7453 H1


title: S6747 A4


title: S1402 F4


title: S601 C3


title: S4807 C1


title: S1402 G4


title: Meroclones_K42_P2E7

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

hyb_protocol: Samples were hybridized to GeneChip™ Human Genome U133 Plus 2.0 Array following the GeneChip 3' IVT PLUS Reagent Kit procedures (Thermo Scientific).

scan_protocol: Arrays were scanned following the GCS 3000 7G User guide (Thermo Scientific).

data_processing: Probe level signals were converted to expression values using the robust multi-array average procedure RMA (Irizarry et al., 2003) comprised in the Bioconductor affy package and a custom chip definition file based on the Entrez gene database (version 23, Dai et al., 2005). Microarray analyses were performed in R (version 3.5.0) using Bioconductor libraries and R statistical packages.

source_name: primary keratinocyte culture

label_protocol: Samples were amplified and labeled according to GeneChip 3' IVT PLUS Reagent Kit Protocol (Thermo Scientific).

growth_protocol: Single cell was plate into 96-well plate, on lethally irradiated 3T3-J2 cells (2.4 X 10^4/cm2) and cultured in 5% CO2 and humidified atmosphere in keratinocyte growth medium (KGM): DMEM and and Ham’s F12 media (3:1 mixture) containing Fetal Bovine Serum (FBS) (10%), insulin (5 mg/ml), adenine (0.18 mM), hydrocortisone (0.4 mg/ml), cholera toxin (CT, 0.1 nM), triiodothyronine (Liothyronine Sodium) (2 nM), epidermal growth factor (EGF, 10 ng/ml), glutamine (4 mM), and penicillin-streptomycin (50 lU/ml)

extract_protocol: Total RNA was isolated from cultured cells using the NucleoSpin ® RNA/Protein kit from Macherey-Nagel.

tag: clonal type

value: M


title: Meroclones_K49_P6C10


title: Meroclones_K5_P12A8


title: Meroclones_K22_P4D4


title: Meroclones_K49_P4D10


title: Meroclones_K49_P4B5


title: Meroclones_K38_P2A7


title: Meroclones_K38_P4H2


title: Meroclones_K5_P7D5


title: Meroclones_K22_P8B2


title: Meroclones_K38_P8C9


title: Meroclones_K5_P11B2


title: Meroclones_K5_P10E12


title: Meroclones_K38_P3G8


title: Meroclones_K49_P2B2


title: Meroclones_K42_P1D9


title: Meroclones_K38_P4B7


title: Meroclones_K42_P5B5


title: Meroclones_K38_P5E1


title: Meroclones_K42_P3B2


title: Meroclones_K38_P7H8


title: Meroclones_K18_P5D6


title: Meroclones_K22_P3D5


title: Meroclones_K18_P3F7


title: Holoclones_K49_P5G2

value: H


title: Holoclones_K49_P2F9


title: Meroclones_K22_P3C11


title: Meroclones_K22_P5H8


title: Meroclones_K18_P3B2


title: Holoclones_K49_P6C5


title: Meroclones_K18_P6H3


title: Holoclones_K5_P5F3


title: Holoclones_K49_P2E3


title: Holoclones_K5_P6F11


title: Holoclones_K5_P8D9


title: Meroclones_K18_P3F3


title: Holoclones_K22_P3B9


title: Holoclones_K42_P1F2


title: Holoclones_K38_P5E8


title: Holoclones_K38_P3B1


title: Holoclones_K22_P4A5


title: Holoclones_K22_P7E6


title: Holoclones_K38_P3G3


title: Holoclones_K38_P4G1


title: Holoclones_K22_P6H11


title: Paraclones_K38_P7B2

value: P


title: Holoclones_K42_P4H8


title: Holoclones_K42_P2G7


title: Holoclones_K22_P4C10


title: Holoclones_K38_P1D10


title: K86_t2

data_processing:
Fastq generation, alignment to the human genome and gene quantification were performed with 10x Cell Ranger v3.1.0.
The UMI count matrix was used for downstream analysis with Seurat v3 and Monocle3 R packages.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with UMI counts for every gene and every cell

source_name: human primary keratinocytes

growth_protocol: Human skin samples were obtained as anonymised surgical waste, typically from abdominoplasty or mammoplasty. Briefly, skin biopsies were minced and trypsinized (0.05% trypsin/0.01%EDTA) at 37_C for 4 hr. Cells were plated (2.5 -3*10^4/cm2) on lethally irradiated 3T3-J2 cells (2.4 X 10^4/cm2) and cultured in 5% CO2 and humidified atmosphere in keratinocyte growth medium (KGM): DMEM and and Ham’s F12 media (3:1 mixture) containing Fetal Bovine Serum (FBS) (10%), insulin (5 mg/ml), adenine (0.18 mM), hydrocortisone (0.4 mg/ml), cholera toxin (CT, 0.1 nM), triiodothyronine (Liothyronine Sodium) (2 nM), epidermal growth factor (EGF, 10 ng/ml), glutamine (4 mM), and penicillin-streptomycin (50 lU/ml) and cultivated on a feeder-layer of lethally irradiated 3T3-J2 cells as described (Dellambra et al., 1998).

extract_protocol:
Keratinocytes were detached with trypsin for 15-20 minutes in order to obtain a single-cell suspension and pelleted in culture medium. Cells were then suspended in 1X PBS with 0.04% BSA and filtered with 70uM cell-filter in order to discard any clamp or cell-cluster. Cell suspension were then visualized and counted with trypan blue using Countess™ II Automated Cell Counter  to get a precise estimation of total number of cells and of cells concentration.   Afterwards we loaded about 10.000 cells of each sample into one channel of the Chromium Chip B using the Single Cell 3' reagent kit v3 (10X Genomic) for Gel bead Emulsion generation into the Chromium system.
Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol. 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following 10xGenomics instruction for read generation, reaching at least 50000 reads as mean reads per cell.

treatment_protocol: Primary human keratinocytes from two different donors (K82 and K86) where harvested at the second passage in culture (t1 dataset). Keratinocyte cultures were serially cultivated and cultures were passaged at full confluence to foster clonal conversion and holoclones exhaustion for 5 passages (t2 dataset).

tag: donor

value: healty donor

tag: timepoint

value: passage 5


title: K82_t2


title: K86_t1

extract_protocol: Keratinocytes were detached with trypsin for 15-20 minutes in order to obtain a single-cell suspension and pelleted in culture medium. Cells were then suspended in 1X PBS with 0.04% BSA and filtered with 70uM cell-filter in order to discard any clamp or cell-cluster. Cell suspension were then visualized and counted with trypan blue using Countess™ II Automated Cell Counter  to get a precise estimation of total number of cells and of cells concentration.   Afterwards we loaded about 10.000 cells of each sample into one channel of the Chromium Chip B using the Single Cell 3' reagent kit v3 (10X Genomic) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol. 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following 10xGenomics instruction for read generation, reaching at least 50000 reads as mean reads per cell.

value: passage 2


title: LLC_TCR_profiling_tet-_rep2

first: Jingyi

last: Wu

state: MA

address: 360 Longwood Ave

department: Department of Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
fastq files were aligned and clonotypes assembled using mixcr analyze amplicon (version 3.0.13) using flags -s mmu --starting-material rna --5-end no-v-primers --3-end c-primers --adapters adapters-present
Mixcr .clonotypes.ALL.txt files of clonotype abundance
Genome_build: Grcm38
Base-calling was performed using bcl2fastq2-v2.20.0

source_name: Lewis lung carcinoma - in vivo

growth_protocol: All cell lines were tested for mycoplasma and cultured in RPMI (VWR) or DMEM media (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
tumors cell suspensions were generated using a Tumor Dissociation Kit (Miltenyi) and the gentleMACS Dissociator (Miltenyi) using the m-TDK-2 program. The resulting cell suspension then passed through a 70 micron filter before lymphocytes were isolated using Lympholyte M cell separation media (Cedarlane), per manufacturer’s instructions. Cells were then enriched for CD45+ cells using CD45 microbeads, mouse (Miltenyi) and the MultiMACS Cell24 Separator Plus (Miltenyi). Cells were then stained in PBS using Live/Dead Fixable Near-IR Dead Cell Stain Kit (1:100, ThermoFischer), H-2Kb MuLV p15E Tetramer (1:10, MBL International), and TrueStain FcX Plus (anti-mouse CD16/32) Antibody (1:1000, BioLegend). Samples were then stained for CD45 (1:100, Biolegend) and CD8 (1:10, MBL International) in MACS Buffer. Samples were pooled and analyzed using a MA900 FACS instrument (Sony), using single-colour compensation controls and fluorescence-minus-one controls for setting gates. Live, cD45+, CD8+, and p15E+ cells were sorted into a RMPI with 50% FBS solution. p15E- cells were also sorted. RNA was  isolated using an RNeasy Micro kit (Qiagen). TCR profiling from RNA was performed using the SMARTer Mouse TCR a/b Profiling Kit (Takara)
llumina sequencing primers were added in a semi-nested approach during TCR amplification; libraries were purified, pooled and then sequenced on an illumina Miseq platform

treatment_protocol: 2*10^6 WT LLC cells were inoculated into both sides of the back of WT recipient mice and expanded in vivo for 14 or 18 days

value: Lewis lung carcinoma - in vivo


title: LLC_TCR_profiling_tet-_rep3


title: LLC_TCR_profiling_tet-_rep1


title: Paraclones_K38_P3G5


title: LLC_TCR_profiling_tet+_rep1


title: Paraclones_K38_P8G9


title: Paraclones_K38_P3F3


title: Paraclones_K5_P8G5


title: Macrophages-apoptotic cells_rep3

city: Frankfurt am Main

first: Anne-Kathrin

last: Knuth

address: Komturstraße 3a

institute: Institut of experimental cancer research in pediatrics

description: 4-3D10_S3_L001_R1_001.fastq.gz.gz_read_counts.txt

data_processing:
data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
umi2index
Trimming: bbduk v35.92
Alignment: STAR Aligner with modifi_x001E_ed ENCODE settings
UMI collapse
Gene Read Counting: HTSeq-count with kit-specic options (FWD)
differential analysis: DESeq2 Pipeline
Genome_build: Mouse (GRCm38)
Supplementary_files_format_and_content: text files containing the normalized read counts

source_name: macrophages

extract_protocol:
RNA of macrophages was isolated using RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer´s instructions. Sequencing libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit with the UMI Second Strand Synthesis Module for QuantSeq (Lexogen, Vienna, Austria). RNA sequencing was performed using a High Output Kit v2 on a NextSeq 500 sequencer (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.5x106 peritoneal macrophages /well were seeded in 24 well plates and co-cultured at a 1 to 1 ratio with NIH 3T3 FV-hCasp-8 cells in a transwell system (6.5 mm transwell with 5 μm pore size; Corning, NY, USA). After an overnight co-culture, 10 nM B/B Homodimerizer was added. 48 hours after treatment, mRNA was isolated.

value: peritoneal macrophages

value: NIH 3T3 FV-hCasp8 cells and dimerizer


title: Macrophages_rep3

description: 4-MF_S12_L001_R1_001.fastq.gz.gz_read_counts.txt

value: dimerizer


title: Macrophages-apoptotic cells_rep4

description: 5-3D10_S11_L001_R1_001.fastq.gz.gz_read_counts.txt


title: Macrophages_rep2

description: 3-MF_S9_L001_R1_001.fastq.gz.gz_read_counts.txt


title: Macrophages-apoptotic cells_rep2

description: 3-3D10_S1_L001_R1_001.fastq.gz.gz_read_counts.txt


title: Macrophages_rep1

description: 2-MF_S8_L001_R1_001.fastq.gz.gz_read_counts.txt


title: Macrophages_rep4

description: 5-MF_S2_L001_R1_001.fastq.gz.gz_read_counts.txt


title: LLC_TCR_profiling_Wt_pd1_ctla4_treatment_rep6

extract_protocol:
RNA was  isolated using an RNeasy Micro kit (Qiagen). TCR profiling from RNA was performed using the SMARTer Mouse TCR a/b Profiling Kit (Takara)
llumina sequencing primers were added in a semi-nested approach during TCR amplification; libraries were purified, pooled and then sequenced on an illumina Miseq platform

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to LLC cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). Cells were then inoculated into both sides of the back of WT recipient mice, expanded in vivo for 14 or 18 days (+/- PD-1/CTLA-4 blockade), and then harvested.


title: Paraclones_K22_P2C1


title: K82_t1


title: Paraclones_K5_P11E4


title: Paraclones_K38_P7B5


title: Paraclones_K38_P2E8


title: Paraclones_K5_P7C9


title: Paraclones_K38_P8A4


title: LLC_TCR_profiling_Wt_pd1_ctla4_treatment_rep3


title: LLC_TCR_profiling_Wt_pd1_ctla4_treatment_rep5


title: LLC_TCR_profiling_Wt_pd1_ctla4_treatment_rep4


title: LLC_TCR_profiling_Wt_pd1_ctla4_treatment_rep1


title: Macrophages-apoptotic cells_rep1

description: 2-3D10_S5_L001_R1_001.fastq.gz.gz_read_counts.txt


title: LLC_TCR_profiling_Wt_no_treatment_rep8


title: LLC_TCR_profiling_Wt_no_treatment_rep5


title: LLC_TCR_profiling_Wt_no_treatment_rep2


title: LLC_TCR_profiling_KO_pd1_ctla4_treatment_rep3


title: LLC_TCR_profiling_Wt_no_treatment_rep7


title: LLC_TCR_profiling_KO_no_treatment_rep8


title: LLC_TCR_profiling_KO_no_treatment_rep9


title: LLC_TCR_profiling_KO_pd1_ctla4_treatment_rep2


title: LLC_TCR_profiling_KO_no_treatment_rep5


title: LLC_TCR_profiling_KO_pd1_ctla4_treatment_rep6


title: LLC_TCR_profiling_KO_no_treatment_rep4


title: LLC_TCR_profiling_KO_no_treatment_rep6


title: LLC_TCR_profiling_Wt_no_treatment_rep6


title: LLC_TCR_profiling_KO_no_treatment_rep1


title: LLC_TCR_profiling_KO_no_treatment_rep7


title: LLC_TCR_profiling_KO_no_treatment_rep10


title: LLC_TCR_profiling_Wt_no_treatment_rep3


title: LLC_TCR_profiling_Wt_pd1_ctla4_treatment_rep2


title: LLC_TCR_profiling_Wt_no_treatment_rep1


title: LLC_TCR_profiling_Wt_no_treatment_rep4


title: LLC_TCR_profiling_KO_pd1_ctla4_treatment_rep5


title: LLC_TCR_profiling_KO_pd1_ctla4_treatment_rep4


title: LLC_TCR_profiling_KO_pd1_ctla4_treatment_rep1


title: LLC_TCR_profiling_KO_no_treatment_rep2


title: scRNA-seq_TCR_LLC_CD4-CD8pos_setdb1_sg4_no_treatment_rep3

data_processing:
cellranger (version 3.0.1) mkfastq was run on defaults to demultiplex bcl files. Cellranger vdj (version 3.1.0) was used to generate single-cell V(D)J sequences and annotations using cellrangers refdata-cellranger-vdj-GRCm38-alts-ensembl-3.1.0 reference
Cellranger vdj all_contig_annotations.csv file of clonotype abundances
Genome_build: Grcm38
Base-calling was performed using bcl2fastq2-v2.20.0

source_name: CD4/8+ enriched immune cells from Lewis lung carcinoma tumors - in vivo

extract_protocol:
Following harvest of tumors, CD4+/CD8+ immune cells were enriched with positive selection using MACS beads/columns and isolated as single cells using droplet-based instrumentation (10x Chromium).
Single-cell RNA sequencing libraries were constructed with 10x chromium 5' reagents.

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to LLC cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). Cells were then inoculated into the flanks of recipient WT mice, expanded in vivo for 15 days (+/- PD-1/CTLA-4 blockade), and then harvested.


title: scRNA-seq_TCR_LLC_CD4-CD8pos_setdb1_sg4_no_treatment_rep2

value: CD4/8+ enriched immune cells from Lewis lung carcinoma tumors - in vivo


title: scRNA-seq_TCR_LLC_CD4-CD8pos_setdb1_sg4_no_treatment_rep1


title: scRNA-seq_TCR_LLC_CD4-CD8pos_setdb1_sg4_pd1_ctla4_treatment_rep2


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_no_treatment_rep4


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_no_treatment_rep3


title: LLC_TCR_profiling_KO_no_treatment_rep3


title: scRNA-seq_TCR_LLC_CD4-CD8pos_setdb1_sg4_pd1_ctla4_treatment_rep1


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep4


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_no_treatment_rep2


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep3


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep2


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep1


title: OA11

city: NEW YORK

first: MUKUNDAN

last: ATTUR

state: NY

address: 301E, 17TH STREET FL16, RM1609

department: MEDICINE

institute: NYU GROSSMAN SCHOOL OF MEDICINE

hyb_protocol: Five micrograms of total RNA from pooled RNA samples used for double-stranded (ds) cDNA synthesis by the Gibco BRL SuperScript Choice System (Life Technologies). Purified ds cDNA was used for synthesis of biotin-labeled cRNA with the ENZO BioArray High-yield RNA transcript labeling kit (Affymetrix). The biotinylated cRNA was purified with the RNeasy kit (Qiagen), fragmented at 95°C for 35 min for target preparation. Biotinylated fragmented cRNA probes were hybridized in the microarray U133A (Affymetrix, Santa Clara, CA), which contained probe sets of over 15,000 known transcripts and expressed sequence tags (ESTs). Hybridization was performed at 45°C for 16 h in a hybridization oven (Affymetrix). The microarrays were washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.

scan_protocol: Fluorescence intensities were scanned with a GeneArray Scanner (Affymetrix) and image analysis was performed with GCOS (Affymetrix). GeneChip Scanner 3000 (Affymetrix) was used for scanning, and image analysis was performed with GCOS (Affymetrix).

data_processing: Data preprocessing, including normalization, modeling, and “presence/ absence” calls, was determined with dChip software (http://biosun1.harvard.edu/complab/dchip). Genes differentially expressed by articular cartilage were identified by comparing gene expression levels between the two groups.

label: BIOTIN

source_name: KNEE CARTILAGE

label_protocol: Pooling of samples: RNA preparations from a total of 60 different normal and OA donors were used. Five paired sets of RNA preparations of articular cartilage each of five donors in equal quantities were used for analysis. The appropriate pooling of RNA samples had been shown to be statistically valid for microarray experiments. Gene expression profiling was performed with the Affymetrix Human Genome (HG) U133A Arrays (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. The Genechip array U133A is a comprehensive whole human genome expression array with over 14,500 well characterized transcripts.

extract_protocol: The freshly obtained OA cartilage specimens were washed in sterile PBS and the specimens were immediately snap-frozen at in liquid nitrogen, and subsequently stored at –140 °C until RNA extraction. Normal cartilage were procured from NDRI as frozen samples. The 1-2 grams frozen cartilage were milled into fine powder in liquid nitrogen using Freezer Miller (SPEX, Metuchen, NJ, USA). Total RNA was extracted from pulverized cartilage as described previously (Attur et al., FASEB J. 29, 4107–4121 (2015). The powder cartilage (for one g cartilage /10ml of TRI reagent) was incubated  in TRI Reagent (MRC Labs, Cincinnati, OH, USA) for 4 h on a rocker at -4C, and chloroform (10%) 1- 2ml was added and spun at 10,000 rpm for 20min at 4C and the clear aqueous phase was collected in a fresh tube. To the clear aqueous phase, add 0.25 volume of high salt solution [0.8M sodium citrate and 1.2M Nacl (Molecular research center (MRC)] and 0.25 volume of isopropanol per 1ml of Trizol used and mix by inverting several times. Spin immediately at maximum speed for 30min at 4oC.The liquid phase has to be removed carefully and do not disturb the RNA pellet (at this time pellet is very loose). The pellet is dissolved in 100-200ul RNAse few water. The RNA pellet was further cleaned and purified using Qiagen RNeasy mini kit according to the manufacturer’s RNA clean-up protocol (Qiagen, Valencia, CA, and USA). Quality and quantity of RNA were confirmed using a Beckman Spectrophotometer

treatment_protocol: HUMAN NORMAL AND OSTEOARTHRITIC KNEE  CARTILAGE ISOLATED PATIENTS UNDERGOING KNEE REPLACEMENT SURGERY.

tag: disease state

value: LATE STAGE OA CARTILAGE


title: OA10


title: OA2


title: scRNA-seq_TCR_LLC_CD4-CD8pos_setdb1_sg4_pd1_ctla4_treatment_rep3


title: OA9


title: OA8


title: N2

value: NORMAL CARTILAGE


title: N4


title: N8


title: N6


title: N7


title: scRNA-seq_gex_LLC_CD4-CD8pos_setdb1_sg4_no_treatment_rep2

data_processing:
cellranger (version 3.0.1) mkfastq was run on defaults to demultiplex bcl files. Cellranger counts was used to generate filtered_feature_matrix.h5
cellranger filtered_feature_matrix .h5
Genome_build: Grcm38
Base-calling was performed using bcl2fastq2-v2.20.0


title: scRNA-seq_TCR_LLC_CD4-CD8pos_control_sg5_no_treatment_rep1


title: scRNA-seq_gex_LLC_CD4-CD8pos_setdb1_sg4_no_treatment_rep3


title: scRNA-seq_gex_LLC_CD4-CD8pos_setdb1_sg4_no_treatment_rep1


title: scRNA-seq_gex_LLC_CD4-CD8pos_setdb1_sg4_pd1_ctla4_treatment_rep3


title: scRNA-seq_gex_LLC_CD4-CD8pos_setdb1_sg4_pd1_ctla4_treatment_rep2


title: scRNA-seq_gex_LLC_CD4-CD8pos_setdb1_sg4_pd1_ctla4_treatment_rep1


title: OA3


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_no_treatment_rep2


title: 0505382H BL day 0

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description: PAXgene Sample

hyb_protocol: Standard Illumina hybridization protocol for HumanHT-12_V4 BeadChips.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the neqc function with limma in R

source_name: Blood

label_protocol: Biotinylated cRNA was oligo-dT primed and prepared with the Illumina TotalPrep RNA amplification kits (Ambion).

extract_protocol: Total RNA was extracted using Qiagen's PreAnalytix PAXgene Blood RNA kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Globin removal was conducted with ThermoFisher's GLOBINclear kit. Quality control was performed with Bio-Rad's Experion.

tag: hiv status

value: HIV Positive

tag: donor id

tag: timepoint unit

value: day

tag: visit

value: BL

tag: age in years


title: 0360675B BL day 0

description: PAXgene Sample


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_no_treatment_rep1


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep4


title: 0361196G V1 wk 3

description: PAXgene Sample

value: wk


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep3


title: 8501845F V2 wk 4

description: PAXgene Sample


title: 8501809A V1 wk 3

description: PAXgene Sample


title: 0503291A V1 wk 3

description: PAXgene Sample


title: 0450398B V1 wk 3

description: PAXgene Sample