title: UPN1 PrePost Not T Enriched

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 6.0.1).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 6.0.1) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each CITE-seq sample using antibody barcode patterns from TotalSeq.
Assembly: GRCh38
Supplementary files format and content: *_GEX.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_FB.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_VDJ.csv CellRanger h5 Gene by Cell Matrix


title: UPN3 PrePost T Enriched

status: Public on Jun 26 2023

type: SRA

city: New York

first: Sanam

last: Shahid

state: New York

address: 1275 York Avenue

department: Department of Pediatrics

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow Aspirate

extract_protocol:
Frozen human bone marrow specimens were thawed and transferred into 5mL polypropylene FACS tubes and resuspended in 4mL PBS + 2mM EDTA + 2% FBS (staining buffer). Cell suspensions were centrifuged at 500g for 5 minutes at 4°C and supernatant was discarded (all subsequent wash steps performed the same way). Cell pellets were re-suspended in staining buffer and counted. For each sample with > 106 live cells, 70% was used for T cell sorting (described below). The remaining 30% of the sample, or the entire sample for those with < 106 live cells, were washed and proceeded to dead cell removal (Miltenyi Biotec). Dead cells were depleted according to manufacturer’s instructions, with the exception of the incubation period shortened to 5 minutes and column washes reduced to 3 times. The live cell fraction was washed, resuspended in staining buffer, and counted. Samples were re-suspended in PBS + 2% FBS (labeling buffer) and Human FcR Blocking Reagent (1:50, Miltenyi Biotec) and incubated on ice for 5 minutes. Samples were tagged with cell hashing (Stoeckius et al., 2018) oligo-tagged antibodies (TotalSeq-C0251 anti-human hashtag 1 antibody and TotalSeq-C0252 anti-human hashtag 2 antibody, BioLegend) according to manufacturer’s instructions. After tagging, samples were washed 3 times in labeling buffer, and then each patient’s samples were pooled together and washed. Samples were re-suspended in labeling buffer and Human FcR Blocking Reagent (1:50, Miltenyi Biotec) and incubated on ice for 5 minutes. CITE-Seq antibodies (TotalSeq-C Human Universal Cocktail, BioLegend) were stained according to manufacturer’s instructions (https://cite-seq.com/protocol/) using the above described labeling buffer for all steps. After staining, samples were washed 3 times in labeling buffer and resuspended at a concentration of 103 cells per μL in cold PBS + 0.04% BSA (sequencing buffer).
Fresh cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following quality control (QC), the single cell suspension was loaded onto a Chromium Next GEM Chip K (10X Genomics PN 1000286). GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 2,000-14,000 cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 13-14 cycles, and 38-50ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 S1 or S2 Reagent Kit (100 or 200 cycles) (Illumina). An average of 263 million paired reads were generated per sample.

tag: tissue

value: Bone Marrow Aspirate

tag: disease state

value: AML


title: UPN2 PrePost Not T Enriched


title: UPN1 Pre T Enriched VDJ

library_source: transcriptomic

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 6.0.1).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 6.0.1) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each CITE-seq sample using antibody barcode patterns from TotalSeq.
Assembly: GRCh38
Supplementary files format and content: *_GEX.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_FB.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_VDJ.csv CellRanger h5 Gene by Cell Matrix
Library strategy: VDJ-seq


title: HD Not T Enriched


title: RPTEC cells, WT, lentiviral transduction, PRRX1, rep1

status: Public on Jul 12 2023

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

data_processing:
Sequence reads were quantified and mapped to reference transcripts using Salmon v1.9.0
Estimated raw counts were extracted using tximport v1.14.2. The counts is normalized by VST (variance stabilizing transformation).
Differential analysis is then performed by DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

source_name: RPTEC

growth_protocol: RPTEC epithelial cells were maintained in DMEM:F12 supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, MEM sodium pyruvate, RPTEC growth kit supplement A 5ml and supplement B 8ml. 250 ug/ml G418 is used for maintaining selection of hTERT. SETD2 expression is maintained in rescue cell lines using 5ug/ml blasticidin.

extract_protocol:
RNA was extracted using Trizol and chloroform. 3 ug of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using TruSeq Stranded mRNA Kit following manufacturer's protocols.

treatment_protocol: For inducing mesenchymal differentiation, RPTEC WT cells were pretreated with 2%FBS for 24h followed by 10ng/ml TGFβ treatment for 72h. WT and KO cells treated with 2%FBS are used as control. Rescue cells were cultured in regular media containing 10%FBS.

tag: cell line

value: RPTEC

tag: cell type

value: Human renal epithelial cells

tag: genotype

tag: treatment

value: Regular media

tag: time


title: UPN2 Pre T Enriched


title: RPTEC cells, KO2, untreated, rep1


title: UPN3 PrePost Not T Enriched


title: UPN4 PrePost Not T Enriched


title: w3_Met_Panc

status: Public on May 02 2023

type: genomic

description: DNA methylation

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Illumina MethylationEPIC (GPL21145) was processed through 'minfi' in R and normalized using SWAN. Avergae beta values in Series supplementary file.

label: Cy5, Cy3

molecule: genomic DNA

source_name: Metastatatic

label_protocol: Illumina protocol

extract_protocol: DNA methylation from multi-region normal kidney and ccRCC tumors

value: Pancreas

value: Metastatatic

tag: age

tag: Sex

value: F


title: m12_B09.1

description: DNA methylation

source_name: Tumor

value: Kidney

value: mt

value: M

tag: nucleargrade

tag: nucleargradegrosscategorical

tag: nucleargradeperregion

tag: nucleargradeperregioncategorical

tag: tumorstagegross

tag: nodalstagegross

tag: mstagegross

tag: necrosisgross

value: No

tag: necrosisperregion

value: A

tag: alive

value: Y

tag: followup(yearsaftersurgery)

tag: ssigngross

tag: ssignperregion

tag: ssignperregioncategorical


title: m12_B07.3

description: DNA methylation

tag: tissue


title: m12_B07.2

description: DNA methylation

tag: age


title: m12_B09.3

description: DNA methylation

tag: Sex


title: m12_B07.1

description: DNA methylation

tag: nucleargrade


title: UPN3 PrePost T Enriched VDJ

tag: disease state


title: HD Not T Enriched CITE

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 6.0.1).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 6.0.1) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each CITE-seq sample using antibody barcode patterns from TotalSeq.
Assembly: GRCh38
Supplementary files format and content: *_GEX.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_FB.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_VDJ.csv CellRanger h5 Gene by Cell Matrix
Library strategy: CITE-seq


title: m12_B06.3

description: DNA methylation

tag: nucleargradegrosscategorical

tag: nucleargradeperregion


title: HD T Enriched


title: UPN4 PrePost T Enriched


title: m12_B06.2

description: DNA methylation

tag: nucleargradeperregioncategorical

tag: tumorstagegross


title: m11_A06.2

description: DNA methylation

tag: nodalstagegross

tag: mstagegross

value: Yes


title: m11_A06.3

description: DNA methylation

tag: necrosisgross

tag: necrosisperregion


title: UPN1 Pre T Enriched


title: m11_A06.1

description: DNA methylation

tag: alive

tag: followup(yearsaftersurgery)


title: m11_A05.4

description: DNA methylation

tag: ssigngross

tag: ssignperregion


title: m12_B03.3

description: DNA methylation

tag: tissue

tag: ssignperregioncategorical


title: m12_B06.1

description: DNA methylation

tag: age

tag: Sex


title: m11_A05.3

description: DNA methylation

tag: nucleargrade


title: m11_A04.2

description: DNA methylation

tag: nucleargradegrosscategorical


title: m11_A05.5

description: DNA methylation

tag: nucleargradeperregion


title: m12_B03.2

description: DNA methylation

tag: nucleargradeperregioncategorical


title: m10_A08.4

description: DNA methylation

tag: tumorstagegross

value: P


title: m10_A08.3

description: DNA methylation

value: Missing

tag: nodalstagegross


title: m11_A05.2

description: DNA methylation

tag: mstagegross


title: m11_A05.1

description: DNA methylation

tag: necrosisgross


title: m10_A06.1

description: DNA methylation

tag: necrosisperregion


title: m10_A06.3

description: DNA methylation

tag: alive


title: m10_A08.2

description: DNA methylation

tag: followup(yearsaftersurgery)


title: m10_A06.4

description: DNA methylation

tag: ssigngross


title: m10_A08.1

description: DNA methylation

tag: ssignperregion


title: m10_A06.2

description: DNA methylation

tag: tissue


title: m11_A04.1

description: DNA methylation

tag: ssignperregioncategorical


title: m10_A05.2

description: DNA methylation

tag: age


title: m10_A05.3

description: DNA methylation

tag: Sex


title: m10_A05.1

description: DNA methylation

tag: nucleargrade


title: m9_A08.6

description: DNA methylation

tag: nucleargradegrosscategorical

value: N


title: m9_A08.5

description: DNA methylation

tag: nucleargradeperregion


title: m12_B03.1

description: DNA methylation

tag: nucleargradeperregioncategorical


title: m9_A08.4

description: DNA methylation

tag: tumorstagegross


title: m9_A08.2

description: DNA methylation

tag: nodalstagegross


title: m9_A08.1

description: DNA methylation

tag: mstagegross


title: m9_A10.5

description: DNA methylation

tag: necrosisgross


title: m9_A10.4

description: DNA methylation

tag: necrosisperregion


title: m9_A10.3

description: DNA methylation

tag: alive


title: m9_A08.3

description: DNA methylation

tag: followup(yearsaftersurgery)


title: m8_A06.3

description: DNA methylation

tag: ssigngross


title: m8_A06.2

description: DNA methylation

tag: ssignperregion


title: m10_A05.4

description: DNA methylation

tag: tissue


title: m8_A05.3

description: DNA methylation

tag: ssignperregioncategorical


title: m9_A10.2

description: DNA methylation

tag: age


title: m9_A10.6

description: DNA methylation

tag: Sex


title: m8_A05.4

description: DNA methylation

tag: nucleargrade


title: m8_A04.4

description: DNA methylation

tag: nucleargradegrosscategorical


title: m8_A04.3

description: DNA methylation

tag: nucleargradeperregion


title: m8_A04.1

description: DNA methylation

tag: nucleargradeperregioncategorical


title: m8_A05.2

description: DNA methylation

tag: tumorstagegross


title: m9_A10.1

description: DNA methylation

tag: nodalstagegross


title: m7_A03.1

description: DNA methylation

value: Nx

tag: mstagegross


title: m8_A05.1

description: DNA methylation

tag: necrosisgross


title: m8_A04.2

description: DNA methylation

tag: necrosisperregion


title: m7_A04.4

description: DNA methylation

tag: alive


title: m7_A04.3

description: DNA methylation

tag: followup(yearsaftersurgery)


title: m7_A04.1

description: DNA methylation

tag: ssigngross


title: m7_A03.5

description: DNA methylation

tag: ssignperregion


title: m7_A04.2

description: DNA methylation

tag: tissue


title: m7_A03.6

description: DNA methylation

tag: ssignperregioncategorical


title: m7_A03.4

description: DNA methylation

tag: age


title: m7_A03.3

description: DNA methylation

tag: Sex


title: m7_A03.2

description: DNA methylation

tag: nucleargrade


title: w6_A08.2

description: DNA methylation

value: wt

tag: nucleargradegrosscategorical


title: m8_A06.1

description: DNA methylation

tag: nucleargradeperregion


title: w6_A08.4

description: DNA methylation

tag: nucleargradeperregioncategorical


title: m8_A06.4

description: DNA methylation

tag: tumorstagegross


title: w6_A08.3

description: DNA methylation

tag: nodalstagegross


title: w6_A07.4

description: DNA methylation

tag: mstagegross


title: w6_A08.1

description: DNA methylation

tag: necrosisgross


title: w6_A05.4

description: DNA methylation

tag: necrosisperregion


title: w6_A07.3

description: DNA methylation

tag: alive


title: w6_A07.1

description: DNA methylation

tag: followup(yearsaftersurgery)


title: w6_A05.1

description: DNA methylation

tag: ssigngross


title: w6_A07.2

description: DNA methylation

tag: ssignperregion


title: w5_B09.2

description: DNA methylation

tag: tissue


title: w5_B09.1

description: DNA methylation

tag: ssignperregioncategorical


title: w5_B07.3

description: DNA methylation

tag: age


title: w5_B09.3

description: DNA methylation

tag: Sex


title: w6_A05.2

description: DNA methylation

tag: nucleargrade


title: w5_B06.3

description: DNA methylation

tag: nucleargradegrosscategorical


title: w5_B07.2

description: DNA methylation

tag: nucleargradeperregion


title: w6_A05.3

description: DNA methylation

tag: nucleargradeperregioncategorical


title: w5_B06.1

description: DNA methylation

tag: tumorstagegross


title: w5_B07.1

description: DNA methylation

tag: nodalstagegross


title: w5_B06.2

description: DNA methylation

tag: mstagegross


title: w5_B05.3

description: DNA methylation

tag: necrosisgross


title: w5_B05.1

description: DNA methylation

tag: necrosisperregion


title: w4_A08.3

description: DNA methylation

tag: alive


title: w5_B05.2

description: DNA methylation

tag: followup(yearsaftersurgery)


title: w4_A08.2

description: DNA methylation

tag: ssigngross


title: w4_A08.1

description: DNA methylation

tag: ssignperregion


title: w4_A07.4

description: DNA methylation

tag: tissue


title: w4_A07.2

description: DNA methylation

tag: ssignperregioncategorical


title: w4_A07.1

description: DNA methylation

tag: age


title: w4_A07.3

description: DNA methylation

tag: Sex


title: w4_A04.1

description: DNA methylation

tag: nucleargrade


title: w4_A03.2

description: DNA methylation

tag: nucleargradegrosscategorical


title: w4_A04.2

description: DNA methylation

tag: nucleargradeperregion


title: w4_A04.3

description: DNA methylation

tag: nucleargradeperregioncategorical


title: w3_B07.4

description: DNA methylation

tag: tumorstagegross


title: w3_B07.2

description: DNA methylation

tag: nodalstagegross


title: w3_B06.4

description: DNA methylation

tag: mstagegross


title: w3_B07.3

description: DNA methylation

tag: necrosisgross


title: w3_B06.2

description: DNA methylation

tag: necrosisperregion


title: w4_A03.1

description: DNA methylation

tag: alive


title: w3_B02.2

description: DNA methylation

tag: followup(yearsaftersurgery)


title: w3_B06.3

description: DNA methylation

tag: ssigngross


title: w3_B07.1

description: DNA methylation

tag: ssignperregion


title: w3_B02.4

description: DNA methylation

tag: tissue


title: w2_C06.4

description: DNA methylation

tag: ssignperregioncategorical


title: w2_C06.2

description: DNA methylation

tag: age


title: w2_C04.3

description: DNA methylation

tag: Sex


title: w2_C04.2

description: DNA methylation

tag: nucleargrade


title: w2_C06.1

description: DNA methylation

tag: nucleargradegrosscategorical


title: w2_C03.3

description: DNA methylation

tag: nucleargradeperregion


title: w2_C03.2

description: DNA methylation

tag: nucleargradeperregioncategorical


title: w1_A10.1

description: DNA methylation

tag: tumorstagegross


title: w2_C03.1

description: DNA methylation

tag: nodalstagegross


title: w1_A08.2

description: DNA methylation

tag: mstagegross


title: w1_A10.2

description: DNA methylation

tag: necrosisgross


title: w3_B02.1

description: DNA methylation

tag: necrosisperregion


title: w3_B06.1

description: DNA methylation

tag: alive


title: w3_B02.3

description: DNA methylation

tag: followup(yearsaftersurgery)


title: w2_C06.3

description: DNA methylation

tag: ssigngross


title: w1_A07.3

description: DNA methylation

tag: ssignperregion


title: w1_A07.1

description: DNA methylation

tag: tissue


title: w1_A06.3

description: DNA methylation

tag: ssignperregioncategorical


title: w1_A07.2

description: DNA methylation

tag: age


title: N8.10

description: DNA methylation

source_name: Normal

value: Normal

tag: Sex


title: N8.08

description: DNA methylation

tag: nucleargrade


title: N8.07

description: DNA methylation

tag: nucleargradegrosscategorical


title: w2_C04.4

description: DNA methylation

tag: nucleargradeperregion


title: w2_C03.4

description: DNA methylation

tag: nucleargradeperregioncategorical


title: w1_A06.1

description: DNA methylation

tag: tumorstagegross


title: w1_A03.2

description: DNA methylation

tag: nodalstagegross


title: N8.09

description: DNA methylation

tag: mstagegross


title: N8.05

description: DNA methylation

tag: necrosisgross


title: N8.03

description: DNA methylation

tag: necrosisperregion


title: N8.04

description: DNA methylation

tag: alive


title: w1_A06.2

description: DNA methylation

tag: followup(yearsaftersurgery)


title: N8.06

description: DNA methylation

tag: ssigngross


title: N8.02

description: DNA methylation

tag: ssignperregion


title: N8.01

description: DNA methylation

tag: tissue


title: N5.10

description: DNA methylation

tag: ssignperregioncategorical


title: w1_A08.1

description: DNA methylation

tag: age


title: w1_A07.4

description: DNA methylation

tag: Sex


title: N5.08

description: DNA methylation

tag: nucleargrade


title: N5.09

description: DNA methylation

tag: nucleargradegrosscategorical


title: N5.04

description: DNA methylation

tag: nucleargradeperregion


title: N5.05

description: DNA methylation

tag: nucleargradeperregioncategorical


title: N5.02

description: DNA methylation

tag: tumorstagegross


title: N5.03

description: DNA methylation

tag: nodalstagegross


title: N5.01

description: DNA methylation

tag: mstagegross


title: N4.08

description: DNA methylation

tag: necrosisgross


title: N4.10

description: DNA methylation

tag: necrosisperregion


title: N4.09

description: DNA methylation

tag: alive


title: N4.06

description: DNA methylation

tag: followup(yearsaftersurgery)


title: N4.07

description: DNA methylation

tag: ssigngross


title: N4.04

description: DNA methylation

tag: ssignperregion


title: N4.05

description: DNA methylation

tag: tissue


title: N4.01

description: DNA methylation

tag: ssignperregioncategorical


title: Human C9, small RNA

status: Public on Mar 22 2023

city: Baltimore

first: Brittney

last: Williams

state: Maryland

address: 22 South Greene St, S11C00

department: Anesthesiology

institute: University of Maryland Baltimore

data_processing:
Raw reads and counts were determined for small RNA
Normalization was performed using cel-mir-39-spike in for human and mouse samples and counts were averaged across all human and mouse samples, respectively
A normilization factor for cel-mir-39-spike was calculated within each individual sample and then applied to the raw read count to generate the processed files
Supplementary files format and content: .txt files for small RNA species for each sample

source_name: Plasma

extract_protocol:
RNA was isolated using Trizol LS from 100 µl of cell-free plasma and was analyzed by an Agilent 2100 Bioanalyzer with the Small RNA kit
Libraries were sequenced on an Illumina HiSeq2500 using six microliters of each RNA solution and used for small RNA sequencing library preparation.
small RNAseq, Library creation using  Norgen Biotek Small RNA Library Prep Kit for miRNA and exceRpt small RNA-seq Pipeline (v4.6.2)

value: Plasma

tag: treatment

value: Control


title: Human C8, small RNA


title: Human C10, small RNA


title: Human C4, small RNA


title: N5.07

description: DNA methylation

tag: age

tag: Sex


title: Human C3, small RNA


title: N5.06

description: DNA methylation

tag: nucleargrade

tag: nucleargradegrosscategorical


title: Human C7, small RNA


title: Human C5, small RNA


title: N4.02

description: DNA methylation

tag: nucleargradeperregion

tag: nucleargradeperregioncategorical


title: Human C2, small RNA


title: Human C1, small RNA


title: female mESC bulk, DMSO, rep3

status: Public on Feb 14 2023

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: flexbar --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcode-unassigned samplebarcode.fasta (using sample barcodes: female_mESC_bulk_DMSO_1: NNNNNAAGCTANNNN; female_mESC_bulk_DMSO_2: NNNNNATTGGCNNNN; female_mESC_bulk_DMSO_3: NNNNNGATCTGNNNN; female_mESC_bulk_DMSO_4: NNNNNTCAAGTNNNN)
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --sjdbGTFfile gencode.vM23.primary_assembly.annotation.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.9), Bedtools (v2.27.1): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.0.0) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --method unique --random-seed=100
Extraction of reads with C>T mutations: CTK (v1.1.3) with non-default parameters: parseAlignment.pl -v --min-len 15 --mutation-file SAMPLE.cims.mutation.tsv SAMPLE.duprm.sam; cat SAMPLE.cims.mutation.tsv | awk '{if($6=="+" && $8=="C" && $9==">" && $10=="T" || $6=="-" && $8=="G" && $9==">" && $10=="A") {print $0}}' | cut -f 1-6 > SAMPLE.C2T.bed
Remove reads with C>T mutations from BAM files: basic Bash, Samtools (v1.9): awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.C2T.bed SAMPLE.duprm.sam | samtools view -b - > SAMPLE.duprm.noC2T.bam
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.noC2T.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.noC2T.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.noC2T.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Assembly: GRCm38.p6 (Gencode release M23)
Supplementary files format and content: bigWig (crosslink events per position)
Library strategy: miCLIP2

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Female mouse embryonic stem cells (mESC) were taken from a previous publication (PMID: 24506884).  Cells were cultured in 2i/LIF medium. Briefly, 500 ml medium was generated by adding 235 ml of each DMEM/F12 and neurobasal (Gibco; 21331020, 21103049), 7.5 ml BSA solution (7.5%, ThermoFisher; 11500496), 5 ml penicillin-streptomycin (Gibco; 15140-122), 2 mM L-Glutamin (ThermoSci; 25030024), 100 µM β-mercaptoethanol (Gibco; 21985023), 5 ml mM nonessential amino acids (Gibco; 11140050), 2.5 ml N2 supplement (Gibco; 17502048), 5 ml B27 supplement (Gibco; 17504044), 3 µM CHIR99021 (Sigma; SML1046), 1 µM PD 0325901 (Biomol; 13034-1), 10 ng/ml LIF (IMB Protein Production core facility). Cells were cultured at 37°C  with 5% CO2. Cell culture dishes were coated using gelatin (Sigma; ES-006-B). The medium was exchanged every day and cells were passaged every second day.

extract_protocol:
For RNA extraction, mES cells were washed twice with ice cold 1x PBS and collected on ice. For total RNA isolation the RNeasy Plus Mini Kit (Qiagen) was used following the manufacturer’s instructions. For poly(A) selection, Oligo d(T)25 Magnetic Beads (Thermo Fisher Scientific; 61002) were used following the manufacturer’s instructions. RNA extraction from mice liver was performed using TRIzol reagent (Invitrogen; 15596026) following the manufacturer’s recommended protocol.
For miCLIP2 the protocol from a previous publication was used (PMID: 34157120): Briefly, 1 µg of polyA selected and fragmented RNA was incubated with an m6A antibody [Synaptic Systems, 202 003] and crosslinked twice at 150 mJ/cm² at 254 nm followed by immunoprecipitation with protein A Dynabeads. After stringent washing, the 3’ end of the RNA was dephosphorylated using T4 PNK and subsequently pre-adenylated L3-App linker was ligated. The 5’ end was radioactively labelled and the samples were purified by SDS PAGE and transferred to a nitrocellulose membrane. After exposure to a Fuji film, the protein-RNA complexes were isolated and elution of the RNA was accomplished by proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Reverse transcription was perform for cDNA synthesis using RT primers against the L3-App linker. The cDNA was purified using MyONE Silane bead clean up system and the 5’ linker was ligated. A pre-amplification PCR with 6 cycles was performed and subsequently the samples were size-selected using ProNex beads. To prevent overamplification of the library, the PCR cycles were optimised to a minimum. For the preparative PCR, the minimum amount of PCR cycles was used followed by a second size selection step using ProNex beads. Libraries were profiled in a High Sensitivity D1000 ScreenTape on a Tape station 2200 (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples in an experiment were pooled in equimolar ratio and sequenced on one NextSeq 500 High Output Flowcell, 75 cycle kit.

treatment_protocol: Cells were treated with medium supplemented with DMSO 0.2% (v/v) for 9 h.

tag: cell line

tag: cell type

value: DMSO

tag: gender

value: female


title: female mESC bulk, DMSO, rep2

value: Female mouse embryonic stem cells (mESC)


title: Human C6, small RNA


title: Th1 - Aiolos KO - biol rep 3 (ATAC-seq)

status: Public on Feb 01 2023

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Avenue, 740 Biomedical Research Tower

institute: The Ohio State University

library_source: genomic

data_processing:
Adapters were trimmed using cutadapt 2.6
Aligned using bowtie 2.4.1
Graphed for visualzation using deepTools bamCoverage 3.3.0 with binSize set to 50 and coverage set to CPM
Peaks were called using MACS2 callpeak
Assembly: mm10
Supplementary files format and content: bigwig (.bw) format, for mm10

source_name: CD4+ T cells

growth_protocol: Naïve WT or Ikzf3-/- CD4+ T cells were cultured in complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich]) under Th1 (5ug/mL anti-IL-4, 5ng/mL IL-12, 50U/mL IL-2) or Tfh (5ug/mL anti-IL-4, 100ng/mL IL-6) polarizing conditions on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL) for 3 days.

extract_protocol:
As described in PMID: 28846090 (Corces et al. Nature Methods 2017)
paired end; prepared using the Illumina Nextera Library Prep kit (paired files were used to generate .bam files, provided)

tag: strain

tag: genotype

value: WT

value: CD4+ T cells

tag: treatment (stimulation)

value: Naïve CD4+ cultured on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL)

tag: treatment (culture_media)

tag: treatment (polarizing_conditions)

value: Th1-polarizing conditions (10ug/mL anti-IL-4, 5ng/mL IL-12, 25U/mL rhIL-2)

tag: time


title: Th1 - Aiolos KO - biol rep 2 (ATAC-seq)

value: complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich])


title: female mESC bulk, DMSO, rep4


title: Th1 - Aiolos KO - biol rep 1 (ATAC-seq)


title: Th1 - WT - biol rep 3 (ATAC-seq)


title: female mESC bulk, DMSO, rep1


title: Th1 - WT - biol rep 2 (ATAC-seq)


title: Th1 - WT - biol rep 1 (ATAC-seq)


title: Tfh - Aiolos KO - biol rep 3 (ATAC-seq)

value: Tfh-polarizing conditions (5ug/mL anti-IL-4, 100ng/mL IL-6)


title: Tfh - Aiolos KO - biol rep 1 (ATAC-seq)


title: Tfh - WT - biol rep 3 (ATAC-seq)


title: Tfh - WT - biol rep 4 (ATAC-seq)


title: N4.03

description: DNA methylation

tag: tissue

value: Kidney

value: F

tag: tumorstagegross

tag: nodalstagegross

tag: mstagegross

tag: necrosisgross

tag: necrosisperregion

tag: alive

tag: followup(yearsaftersurgery)

tag: ssigngross

tag: ssignperregion

tag: ssignperregioncategorical


title: Tfh - WT - biol rep 2 (ATAC-seq)

tag: strain

tag: cell type


title: Tfh - WT - biol rep 1 (ATAC-seq)

tag: genotype

tag: treatment (stimulation)


title: Th2 - Ikzf4 KO2 [JT-KO2]

description: Ikzf4-/- Th2 RNA seq_replicate 2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 (mm10) reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: DESeq2 analysis including normalized counts, log2 fold changes, and p-values; .csv

growth_protocol: Naïve WT or Ikzf4-/- CD4+ T cells were cultured in complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich]) under Th2 (10 ug/mL anti-Ifng, 10 ng/mL IL-4) polarizing conditions on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL) for 3 days. Total RNA was isolated and provided to Azenta Life Sciences for library preparation and downstream analysis.

extract_protocol:
Total RNA was isolated from cell pellets using the Macherey-Nagel Nucleospin RNA isolation kit according to the manufacturer's instructions.
Libraries were generated and sequenced according to standard protocols from Azenta Life Sciences, Inc., to which the samples were sent for library preparation and analysis.

tag: strain background

tag: treatment

value: stimulation; Naïve CD4+ cultured on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL)

tag: culture media

tag: polarizing conditions

value: Th2-polarizing conditions (10 ug/mL anti-Ifng, 10 ng/mL IL-4)

tag: time point


title: Th2 - WT3 [JT-WT3]

description: WT Th2 RNA seq_replicate 3


title: Th2 - Ikzf4 KO1 [JT-KO1]

description: Ikzf4-/- Th2 RNA seq_replicate 1


title: Th2 - WT1 [JT-WT1]

description: WT Th2 RNA seq_replicate 1


title: Th2 - WT2 [JT-WT2]

description: WT Th2 RNA seq_replicate 2


title: Tfh - WT3 (RNA-seq)

description:
WT Tfh RNA seq_replicate 3
Tfh_Differential_expression_analysis_table.csv

growth_protocol: Naïve WT or Ikzf3-/- CD4+ T cells were cultured in complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich]) under Th1 (5ug/mL anti-IL-4, 5ng/mL IL-12, 50U/mL IL-2) or Tfh (5ug/mL anti-IL-4, 100ng/mL IL-6) polarizing conditions on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL) for 3 days. Total RNA was isolated and provided to Azenta Life Sciences for library preparation and downstream analysis.

treatment_protocol:
treatment - stimulation:  Naïve CD4+ cultured on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL)
treatment - culture media:  complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich])
treatment - polarizing conditions:  Tfh-polarizing conditions (10ug/mL anti-IL-4, 100ng/mL IL-6)

tag: treatment (culture media)

value: complete IMDM

tag: treatment (polarizing conditions)

value: Tfh-polarizing conditions

tag: time


title: Tfh - Ikzf3 KO1 (RNA-seq)

description:
Ikzf3-/- Tfh RNA seq_replicate 1
Tfh_Differential_expression_analysis_table.csv

value: cultured on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL)


title: Tfh - WT2 (RNA-seq)

description:
WT Tfh RNA seq_replicate 2
Tfh_Differential_expression_analysis_table.csv


title: Tfh - Ikzf3 KO3 (RNA-seq)

description:
Ikzf3-/- Tfh RNA seq_replicate 3
Tfh_Differential_expression_analysis_table.csv


title: Th1 - Ikzf3 KO3 (RNA-seq)

description:
Ikzf3-/- Th1 RNA seq_replicate 3
Th1_Differential_expression_analysis_table.csv

treatment_protocol:
treatment - stimulation:  Naïve CD4+ cultured on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL)
treatment - culture media:  complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich])
treatment - polarizing conditions:  Th1-polarizing conditions (10ug/mL anti-IL-4, 5ng/mL IL-12, 25U/mL rhIL-2)

value: Th1-polarizing conditions


title: Tfh - Ikzf3 KO2 (RNA-seq)

description:
Ikzf3-/- Tfh RNA seq_replicate 2
Tfh_Differential_expression_analysis_table.csv


title: Tfh - WT1 (RNA-seq)

description:
WT Tfh RNA seq_replicate 1
Tfh_Differential_expression_analysis_table.csv


title: Th1 - Ikzf3 KO2 (RNA-seq)

description:
Ikzf3-/- Th1 RNA seq_replicate 2
Th1_Differential_expression_analysis_table.csv


title: Th1 - WT3 (RNA-seq)

description:
WT Th1 RNA seq_replicate 3
Th1_Differential_expression_analysis_table.csv


title: Tfh - Aiolos KO - biol rep 4 (ATAC-seq)

tag: treatment (culture_media)

tag: treatment (polarizing_conditions)


title: Th1 - WT2 (RNA-seq)

description:
WT Th1 RNA seq_replicate 2
Th1_Differential_expression_analysis_table.csv


title: Th1 - Ikzf3 KO1 (RNA-seq)

description:
Ikzf3-/- Th1 RNA seq_replicate 1
Th1_Differential_expression_analysis_table.csv


title: ACL injured quadricep biopsy M19R

status: Public on Jan 11 2023

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

description: ACL injured quadricep biopsy

data_processing:
Sequenced reads were trimmed from the 3' end based on quality score with a minumum Phred score of 20 and a minumum read length of 25 bp
Trimmed reads were alligned to the hg19 reference genome using STAR 2.7.8a aligner with default parameters.
Aligned reads were quantified to the hg19 reference assembly with requrement of junction reads to match introns and strict paired-end compatibility.  Quantified reads went through a noise reduction filter with maximum feature exclusion set less than or equal to 10.
Filtered counts were normalized per million and tested for statistical significance using DESeq2
All steps were performed using the Partek® Flow® Software.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Skeletal muscle

extract_protocol:
Human quadricep RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
Conducted at NovoGene

tag: tissue

value: Skeletal muscle

value: ACL injured quadricep biopsy


title: Th1 - WT1 (RNA-seq)

description:
WT Th1 RNA seq_replicate 1
Th1_Differential_expression_analysis_table.csv


title: Tfh - Aiolos KO - biol rep 2 (ATAC-seq)


title: ACL injured quadricep biopsy M18R

description: ACL injured quadricep biopsy


title: ACL non-injured quadricep biopsy M19NR

description: ACL non-injured quadricep biopsy

value: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M18NR

description: ACL non-injured quadricep biopsy


title: Th2 - Ikzf4 KO3 [JT-KO3]

description: Ikzf4-/- Th2 RNA seq_replicate 3


title: ACL injured quadricep biopsy M17R

description: ACL injured quadricep biopsy


title: ACL non-injured quadricep biopsy M15NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M17NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M13NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M08NR_b

description: ACL non-injured quadricep biopsy


title: ACL injured quadricep biopsy M13R

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy M11R

description: ACL injured quadricep biopsy


title: ACL non-injured quadricep biopsy M07NR_b

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M11NR

description: ACL non-injured quadricep biopsy


title: ACL injured quadricep biopsy M08R_b

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy M05R

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy M07R_b

description: ACL injured quadricep biopsy


title: ACL non-injured quadricep biopsy M04NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M05NR

description: ACL non-injured quadricep biopsy


title: ACL injured quadricep biopsy A12R_b

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy M04R

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy M02R

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy A05R

description: ACL injured quadricep biopsy


title: ACL non-injured quadricep biopsy M02NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy M01NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy A09NR

description: ACL non-injured quadricep biopsy


title: ACL injured quadricep biopsy A09R

description: ACL injured quadricep biopsy


title: ACL injured quadricep biopsy M15R

description: ACL injured quadricep biopsy


title: Tg mice after MSA-C onset

status: Public on Sep 06 2022

city: Fukuoka

first: Hiroo

last: Yamaguchi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

country: Japan

institute: Neurological Institute, Graduate School of Medical Sciences,  Kyushu University

data_processing:
The sequence data were mapped to mouse reference genome (mm10) and counted using the Cell Ranger (5.0.0) pipeline by 10xGenomics.
The count matrix data were imported to R with Seurat (4.0.6) package and analyzed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RNA counts with barcords.

source_name: cerebellum, brainstem and spinal cord

extract_protocol: RNA was extracted and barcorded using Chromium Single Cell 3' Reagent Kits v3.1

value: CD11b-positive microglia from the brain of Tg mice after MSA-C onset

tag: mouse model

value: multiple system atrophy (MSA)-cerebellar type (MSA-C)

value: cerebellum, brainstem and spinal cord

tag: age

value: 26 weeks

value: Plp1-tTA::tetO- SNCA*A53T


title: ACL non-injured quadricep biopsy A04NR

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy A12NR_b

description: ACL non-injured quadricep biopsy


title: ACL non-injured quadricep biopsy A05NR

description: ACL non-injured quadricep biopsy


title: Tg mice treated with BLZ945

value: CD11b-positive microglia from the brain of BLZ945-treated Tg mice

tag: strain

value: BLZ945, a CSF1R inhibitor


title: Male-3

status: Public on May 06 2022

city: Bronx

first: Marija

last: Kundakovic

state: NY

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

data_processing:
Sequenced reads were mapped using BWA to the mouse genome build mm10, with a quality filter >= 10, and removal of PCR duplicates. .Hi-C files were created by combining replicates and then processed and visualized with Juicebox.
Genome_build: mm10
Supplementary_files_format_and_content: .hic files

source_name: Brain

growth_protocol: Male and female C57BL/6J mice from Jackson Laboratory arrived at seven weeks of age and were housed in same-sex cages (n=4-5 per cage). Mice were habituated for two weeks and were kept on a 12:12h light:dark cycle with ad libitum access to food and water.

extract_protocol:
At 11 weeks of age, male and female animals were sacrificed via cervical dislocation; the head was decapitated,brains were extracted, and bilateral ventral hippocampi were dissected on ice then flash frozen in liquid nitrogen.
The unbiased chromatin conformation capture Hi-C method was performed using the Arima Hi-C kit, as per manufacturer’s instructions

treatment_protocol: Following habituation, the estrous cycle of female animals was tracked daily in the morning (between 9AM and 11AM) for two weeks in order to establish a predictive cycling pattern for each female animal and to ensure that only females with regular cycles were included in the study

tag: cell type

value: Neuronal cells


title: Diestrus-3


title: PTBP iCLIP2 2-500

status: Public on Jun 05 2022

city: Mainz

last: König

address: Ackermannweg 4

department: Biology

institute: Institute of Molecular Biology, Mainz

description:
imb_koenig_2021_07_M_PTB_1_500.v2uniqMD
BW files separated in strands

data_processing:
library strategy: iCLIP2
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 –min-read-length 15 --length-dist --umi-tags --barcode-unassigned samplebarcode.fasta (using sample barcodes: PTBP iCLIP2 1-300 NNNNNACATCGNNNN, PTBP iCLIP2 1-500 NNNNNTGGTCANNNN, PTBP iCLIP2 2-300 NNNNNATTGGCNNNN and PTBP iCLIP2 2-500 NNNNNGATCTGNNNN)
Mapping: STAR (v2.7.3a) with parameters: --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with parameter --method unique
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigWig (crosslink event per position): BAM files were transformed to a BED files using bedtools bamtobed (v2.27.1) considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).

source_name: NALM-6 cells

growth_protocol: Media from cells growing in a 10 cm tissue culture plate was replaced with 6 ml cold PBS and the plate was put on ice.

extract_protocol:
Cells were harvested by scraping and collected by centrifugation at 1000x g for 1 min at 4 °C. The supernatant was subsequently removed and the cell pellets were either snap-frozen and stored or immediately subjected to immunoprecipitation. Protein-RNA complexes were immunoprecipitated by using a monoclonal mouse anti-PTBP1(hnRNP I) antibody from SCBT (sc-56701). Then, RNase digestion was performed by diluted RNase I (Invitrogene) to each sample. Further processing of the sample including RNA extraction was performed according to a previously published protocol (Buchbender, Andreas, et al. Methods 178 (2020): 33-48).
cDNA synthesis was carried out using the Superscript III (Invitrogene) reverse transcriptase according to the manufacturer’s protocol. Subsequently, the cDNA was gel-purified and circularized according to a previously published protocol (Buchbender, Andreas, et al. Methods 178 (2020): 33-48). Next, the cDNA was PCR-amplified and the products were purified and size-selected using the ProNex® chemistry.

treatment_protocol: Cells were irradiated once with 150 mJ/cm2 in a Stratalinker 2400 at 254 nm.

tag: cell line

tag: iclip2 antibody


title: PTBP iCLIP2 1-500

description:
imb_koenig_2021_07_A_PTB_1_500.v2uniqMD
BW files separated in strands


title: Tg mice before MSA-C onset

value: CD11b-positive microglia from the brain of Tg mice before MSA-C onset

value: 22 weeks

tag: genotype


title: PTBP iCLIP2 2-300

description:
imb_koenig_2021_07_M_PTB_1_300.v2uniqMD
BW files separated in strands


title: OvxEB4

data_processing:
Sequenced reads were mapped using BWA to the mouse genome build mm10, with a quality filter >= 10, and removal of PCR duplicates.
Hi-C files were created by combining replicates and then processed and visualized with Juicebox
Genome_build: mm10
Supplementary_files_format_and_content: .hic

source_name: Ventral hippocampal NeuN+ nuclei

growth_protocol: Mice were ovariectomized at eight weeks of age, arrived at nine weeks, then habituated for two weeks prior to injections and tissue collection.

extract_protocol:
At 11 weeks of age and 4 hours after receiving either estradiol benzoate (5ug) or vehicle (1% EtOH in corn oil; s.c.), ovariectomized  female animals were sacrificed via cervical dislocation; the head was decapitated, brains were extracted, and bilateral ventral hippocampi were dissected on ice then flash frozen in liquid nitrogen. NeuN+ (neuronal) nuclei were purified from ventral hippocampal tissue using nuclei isolation and flow cytometry sorting.
The unbiased chromatin conformation capture Hi-C method was performed using the Arima Hi-C kit, as per manufacturer’s instructions.

treatment_protocol: Female C57BL/6J mice from Jackson Laboratory arrived at nine weeks of age and were housed in same-sex cages (n=4-5 per cage). Mice were habituated for two weeks and were kept on a 12:12h light:dark cycle with ad libitum access to food and water.

tag: treatment

value: Estradiol benzoate-injected

tag: surgery

value: Ovariectomized

tag: molecule type

value: Proximally-ligated DNA


title: ACL injured quadricep biopsy M01R

description: ACL injured quadricep biopsy


title: PTBP iCLIP2 1-300

description:
imb_koenig_2021_07_A_PTB_1_300.v2uniqMD
BW files separated in strands


title: Male-2


title: Proestrus-2


title: ACL injured quadricep biopsy A04R

description: ACL injured quadricep biopsy


title: Diestrus-2


title: Male-1


title: Proestrus-1


title: Diestrus-1


title: OvxEB5


title: OvxVeh3

value: Vehicle-injected


status: Public on Jan 07 2022

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
low progression free survival group, patient 9
low.9

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg38 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file contains the raw counts for each gene

source_name: FFPE melanoma tumor

extract_protocol:
Total RNA was extracted using Life Technologies Recover All Total Nucleic Acid Isolation kit- FFPE (AM1975-R10)
Sequencing library preparation was then completed using Kapa RNAseq w/o rRNA removal (R130) libarry preparation kit according to the manufacturer’s instructions

tag: progression-free survival (pfs) rate

value: low

tag: patientid

tag: ldh level

value: elevated


title: OvxEB3


description:
low progression free survival group, patient 11
low.11

value: normal


title: OvxEB2


title: OvxVeh2


title: db/db

status: Public on Jan 01 2022

city: chengdu

first: qian

last: wang

address: renmin road south

country: China

institute: sichuan university

data_processing:
After obtaining the initial sequencing data, we folded the UMI with CellrRanger (version 3.1, 10x Genomics) software to obtain a single-cell gene expression matrix.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar: Tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; Matrix table with raw gene counts for every gene and every cell.

source_name: Gingiva

extract_protocol:
Single cells were suspended in 0.04% non-acetylated BSA (UltraPure BSA, ThermoFisher Scientific) and filtered by Dead Cell Removal kit (#130-090-101, Miltenyi Biotec B.V. &Co.KG) so that debris and dead cell is excluded. Single-cell suspensions were captured using the 10X Genomics Chromium Single Cell 3’ Solution (v3) according to the manufacturer's protocol.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: db/db

value: Gingiva

value: 16 weeks


title: OvxVeh5


title: OvxVeh1


description:
low progression free survival group, patient 10
low.10


title: WT

value: WT


title: OvxVeh4


title: NON_REP2_L001

status: Public on Dec 23 2021

city: Berkeley

first: Jamie

middle: H D

last: Cate

state: CA

address: 2151 Berkeley Way

department: Molecular and Cell Biology/Chemistry

institute: University of California

description: Samples EIF3A/C/B and EIF3B/C PAR-CLIP, nonactivated Jurkat, replicate 2

data_processing:
Library strategy: PAR-CLIP
PAR-CLIP replicate 1 library adaptors have 3' sequence TCGTATGCCGTCTTCTGCTTG. This is preceded by a 5-nt UMI barcode for PCR deduplication. Finally, each eIF3 subunit sample is indicated by a 5-nt barcode.
Barcoding for PAR-CLIP samples: PA=TCACTNNNNN  PB=TCATCNNNNN  PD=TCCACNNNNN  P1=TCCGTNNNNN  P2=TCACTNNNNN where NNNNN is the UMI for PCR deduplication
Clusters of overlapping sequence reads mapped against the human genome version hg38 were generated using the PARalyzer software (Pubmed ID: 21851591) incorporated into the PARpipe pipeline (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/, (Pubmed ID: 30517751) with the settings below. Binding sites were categorized using the Gencode GRCh38.p12 GTF annotations (gencode.v21.annotation.gtf), https://www.gencodegenes.org/human/.
Settings used for PARpipe: Conversion = T>C;   Minimum read count per group = 5;   Minimum read count per cluster = 7;   Minimum read count for kde = 3;   Minimum cluster size = 11;   Minimum conversion locations for cluster = 2;   Minimum conversion count for cluster = 2;   Minimum read count for cluster inclusion = 1;   Minimum read length = 20;   Maximum number of non conversion mismatches = 1;
Genome_build: hg38
Supplementary_files_format_and_content: Excel spreadsheets with tabulated data from the PAR-CLIP experiment or RNA-Seq experiment.

growth_protocol: Cells were maintained in RPMI 1640 Medium (ATCC modification) with 10% FBS (VWR Life Science Seradigm) and 0.01% Penicillin-Streptomycin (10,000 U/mL) (ThermoFisher).

extract_protocol:
The cells were pelleted by centrifugation at 100 x g for 15 min at 4 °C, and the pellet was resuspended in three volumes of NP40 lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% Nonidet P-40 alternative, 0.5 mM dithiothreitol (DTT), 1 Complete Mini EDTA-free Protease Inhibitor Cocktail tablet (Roche)). The cell suspension was then incubated on ice for 10 min, passed through an 18G needle five times, and centrifuged at 13,000 x g for 15 min at 4 °C and RNAs were lightly digested by treatment with MNase (Thermo Scientific) at a final concentration of 0.05 U μl-1 for 20 min at 16 °C. For each PAR-CLIP assay 1000 μL of Dynabeads (Invitrogen) and 800 μL of anti-EIF3B antibody (Bethyl A301-761A) were used. The remaining steps of the PAR-CLIP analysis were performed exactly as described in (Pubmed ID: 25849773, 26463383) with the exception of using MNase at 5 U μL-1 for the on-bead digestion step.
PAR-CLIP cDNA libraries were sequenced on an Illumina HiSeq 2500 platform. To eliminate potential PCR biases during PAR-CLIP library preparation, a random bar code was introduced into the 3’ adapter and all the reads that matched the random barcode were collapsed into single reads.

treatment_protocol: 50 µM of 4-thiouridine was determined as non-toxic to Jurkat cells over the time course of the PAR-CLIP experiments. Jurkat cells seeded at 8 x 10^5 cells ml-1 were treated with 50 µM of 4-thiouridine for 7 hours. Then, the cells were treated with or without 1X Cell Stimulation Cocktail, containing PMA and IONO (ThermoFisher, Cat. #: 00-4970-93) for 5 hours. Cells were then crosslinked on ice with 365 nm UV irradiation at an energy dose of 0.2 J cm-2.

value: T cell leukemia

value: Jurkat Clone E6-1

tag: molecule

value: RNA crosslinked to eIF3


title: CF2

status: Public on Nov 16 2021

city: Iowa city

first: Wenjie

last: Yu

state: IA

address: 200 Hawkins Dr, 6330 PBDB

institute: The University of Iowa

data_processing:
Illumina software HCS HD version 3.4.0 was used for basecalling.
Raw FASTQ reads alignment, filtering, barcode counting, and UMI counting were performed using 10x CellRanger version 3.0.2.
Genome_build: Sscrofa11.1 from RefSeq database. The annotation of about 240 genes were improved based on references from Ensembl, Genbank mRNA databases.
Supplementary_files_format_and_content: HDF5 format files (including raw and filtered files) contain counts for each gene and cell barcode.
Supplementary_files_format_and_content: GTF format file is an improved version of the original Sscrofa11.1.gtf (date as 12/10/2019) file from RefSeq database

organism: Sus scrofa

source_name: Airway submucosal glands

extract_protocol:
Tracheal segments from newborn wild-type and CFTR-/- pigs were collected and kept in cold 1x DPBS. Trachea were cut open at the ventral side in cold 1x DPBS with 0.1% gentamicin. Airway surface epithelial cells were scraped off and the remaining epithelial layer was separated from the cartilage layer of the trachea to explore SMGs. The peeled epithelial layer was transferred into a new dish with cold 1x DPBS with 0.1% gentamicin. Individual SMGs were then dissected off from the epithelial layer into the medium. Dissected SMG tissues were collected and successively dissociated with Collagenase/Hyaluronidase (30 min) and Pronase/DNase (2 hours) medium at 37 oC. After that, dissociation was terminated using cold 1 x DPBS with fetal bovine serum. Cells were further washed with cold 1 x DPBS and filtered with 40-µm tissue strainers. Single cells were spun down and resuspended in 1 x DPBS with 0.4 mg/ml bovine serum albumin at around 1000 cells/µl.
10x Genomics Chromium Single Cell 3’ Reagent Kits v2 system

value: newborn

value: CFTR-/-


title: ACT_REP2_L001

description: Samples EIF3A/C/B  and EIF3B/C PAR-CLIP, activated Jurkat, replicate 2


title: NON_REP2_L002

description: Samples EIF3D/L, EIF3F/E and EIF3G/E/F PAR-CLIP, nonactivated Jurkat, replicate 2


title: CF1


title: ACT_REP2_L002

description: Samples EIF3D/L, EIF3F/E and EIF3G/E/F PAR-CLIP, activated Jurkat, replicate 2


title: Proestrus-3

value: Neuronal cells


title: WT4

value: Wild-type


title: OvxEB1

value: Estradiol benzoate-injected

value: Ovariectomized


title: Huh7.5_HCV_ATAC

status: Public on Sep 23 2021

description: histone modification

data_processing:
RNA-seq raw reads were mapped to hg38. Expression was quantified through Salmon v1.4.0.
ChIP-seq raw reads were mapped to hg38. Peak calling was performed with MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: quant (txt)
Supplementary_files_format_and_content: peak (bed)

source_name: HCV

extract_protocol:
Mnase digested nucleosomes
Nuclei were subjected to transposition at 37 degrees for 30 mins in a thermomixer followed by purification and indexing, as done in PMID: 28846090
see samples
see samples

tag: disease stage

value: HCC

tag: antibody


title: WT2


title: CF3


title: Huh7.5_HCV_H3K4me1

description: histone modification

extract_protocol:
Mnase digested nucleosomes
Libraries were consstructed accroding to manufacturer's instructions
see samples
see samples

value: ab8896, Abcam


title: Huh7.5_HCV_H3K27me3

description: histone modification


title: Huh7.5_HCV_H3K27ac

description: histone modification

value: ab4729, Abcam


title: Huh7.5_HCV_H3K4me3

description: histone modification

value: ab8580, Abcam


title: Huh7.5_input 2

description: histone modification


title: Huh7.5_H3K27ac

description: histone modification

source_name: parent


title: WT3


title: Huh7.5_H3K4me1

description: histone modification


title: Huh7.5_input 1

description: histone modification


title: Huh7.5_ATAC

description: histone modification


title: CF4


title: Hu1545_HCV_ATAC

description: histone modification

value: surrogate normal


title: Hu1545_HCV_H3K27me3

description: histone modification


title: Hu1545_HCV_H3K27ac

description: histone modification


title: Hu1545_HCV_H3K4me1

description: histone modification


title: Hu1545_HCV_H3K4me3

description: histone modification


title: WT1


title: Hu1545_H3K4me3

description: histone modification


title: NJ038

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

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing:
Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package "minfi".
matrix signal intensities value definition: Unmethylated and methylated signal intensities
matrix processed :Average Beta

label: Cy5 and Cy3

source_name: HCV cure NJ038

label_protocol: Standard Illumina Infinium Methylation assay protocol

growth_protocol: All cultured cells were grown in DMEM with 10% FBS.

extract_protocol: Genomic DNA was extracted by proteinase K treatment, phenol:chloroform extraction, and ethanol precipitation.

treatment_protocol: Each cell line (referred to as the ‘parent’ cell line) was electroporated with full-length HCV JFH-1 RNA or JFH-1/GND (replication defective control) and selected with G418 for two weeks). Following establishment of clonal derivatives with stable HCV replication, cells were treated with either interferon-α (Sigma-Aldrich human recombinant interferon-α 407294-5MU; 1200IU/mL every 3 days for 2 weeks) or the direct-acting antiviral (DAA) Telaprevir (Incivek Telaprevir 375mg resuspended in DMSO; 30µM final concentration every 3 days for 2 weeks).

tag: tissue

value: liver

tag: disease

value: HCV cured


title: Hu1545_HCV_input

description: histone modification


title: Hu1545_ATAC

description: histone modification

extract_protocol:
Mnase digested nucleosomes
Nuclei were subjected to transposition at 37 degrees for 30 mins in a thermomixer followed by purification and indexing.
see samples
see samples


title: Hu1545_H3K27me3

description: histone modification


title: Hu1545 HCV IFN 5aza Xia

source_name: HCV IFN 5aza


title: Hu1545 HCV Tela 5aza Xia

source_name: HCV Telaprevir 5aza


title: NJ035

source_name: HCV cure NJ035


title: Hu1545 HCV rep1


title: Huh7.5_H3K27me3

description: histone modification


title: Hu1545 HCV Tela rep1

source_name: HCV Telaprevir


title: Hu1545 HCV Tela rep2


title: Huh75 HCV rep1


title: Hu1545_H3K4me1

description: histone modification


title: Huh7.5_H3K4me3

description: histone modification


title: Hu1545 IFN rep2

source_name: IFN


title: Hu1545 HCV IFN rep1

source_name: HCV IFN


title: Huh75 HCV IFN rep2


title: Huh75 IFN rep2


title: Hu1545 IFN rep1


title: Huh75 HCV IFN rep1


title: Hu1545_H3K27ac

description: histone modification


title: NJ034

source_name: HCV cure NJ034


title: NJ037

source_name: HCV cure NJ037


title: Hu1545 Tela rep1

source_name: Tela


title: Hu1545_input

description: histone modification


title: Hu1545 HCV rep2


title: NJ036

source_name: HCV cure NJ036


title: Huh75 Tela rep1

source_name: Telaprevir


title: Huh75 HCV Tela rep1


title: Huh75 Tela rep2


title: Huh75 rep2


title: Hu1545 rep1


title: Huh75 rep1


title: Huh75 IFN rep1


title: Hu1545 rep2


title: Huh75 HCV rep2


title: Hu1545_HCV_IFN_5-azadC

description: Gene expression

source_name: HCV IFN 5-azadC

extract_protocol:
trizol
Libraries were constructed according to illumina's instructions for TruSeq stranded mRNA
see samples
see samples


title: Hu1545 HCV IFN rep2


title: Huh75 HCV Tela rep2


title: Hu1545_HCV_DAA_5-azadC

description: Gene expression

source_name: HCV Telaprevir 5-azadC


title: ND10

description: Gene expression

value: liver tissue

value: normal


title: ND9

description: Gene expression


title: Huh7.5_HCV_DAA_1

description: Gene expression


title: Huh7.5_HCV_DAA_2

description: Gene expression


title: Huh7.5_HCV_IFN_2

description: Gene expression


title: Huh7.5_HCV_IFN_1

description: Gene expression


title: Huh7.5_DAA_1

description: Gene expression


title: Huh7.5_IFN_2

description: Gene expression


title: Huh7.5_HCV_1

description: Gene expression


title: Huh7.5_HCV_2

description: Gene expression


title: Hu1545 Tela rep2


title: Huh7.5_2

description: Gene expression


title: Hu1545_HCV_DAA_2

description: Gene expression


title: Hu1545_HCV_IFN_2

description: Gene expression


title: Hu1545_DAA_2

description: Gene expression


title: Hu1545_HCV_DAA_1

description: Gene expression


title: Hu1545_IFN_1

description: Gene expression


title: Hu1545_HCV_IFN_1

description: Gene expression


title: Huh7.5_1

description: Gene expression


title: Hu1545_IFN_2

description: Gene expression


title: Huh7.5_IFN_1

description: Gene expression


title: Hu1545_DAA_1

description: Gene expression


title: Hu1545_2

description: Gene expression


title: Hu1545_HCV_2

description: Gene expression


title: Hu1545_1

description: Gene expression


title: EWIma7_Tum_meta_liver

status: Public on Sep 08 2021

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Reads were trimmed with Atropos
Mapping and gene quantification were performed with STAR version 2.6.1a_08-27 againt human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
DESEQ2 DESeq2_1.24.0 was used to perform differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with raw counts for each genes.

source_name: mesenchymal stem cells derived from an EwS patient (MSCPat)

growth_protocol: MSC_Pat, hMPCs and EWIma were cultured in aMEM (Life Technologies, 22561021) supplemented with 10% fetal bovine serum (MSC grade, Life Technologies, 12662029) and glutamine at 10mM (Life Technologies, 25030024). In addition, MSC_Pat and hMPCs were supplemented with 2 ng/mL recombinant human FGF (R&D Systems, 233-FB-025). Two days before performing the ChIP experiments, cells were seeded at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.

extract_protocol:
RNA was extracted using RNeasy plus mini kit (74134, Qiagen) following manufacturer instructions
RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library.

value: Mut


title: EWIma5_Tum_leg


title: EWIma7_Tum_leg


title: Huh7.5_DAA_2

description: Gene expression


title: EWIma5_Tum1_meta_liver


title: EWIma5


title: EWIma_cloneG12


title: EWIma30


title: EWIma7


title: EWIma2


title: EWIma13


title: EWIma14


title: EWIma26


title: EWIma15


title: Hu1545_HCV_1

description: Gene expression

source_name: HCV


title: EWIma31


title: EWIma8


title: EWIma12


title: EWIma25


title: EWIma9


title: EWIma11


title: EWIma4


title: D310T15: MSC_Pat_R3

status: Public on Aug 18 2021

growth_protocol: MSC_Pat, hMPCs and EWIma1 were cultured in aMEM (Life Technologies, 22561021) supplemented with 10% fetal bovine serum (MSC grade, Life Technologies, 12662029) and glutamine at 10mM (Life Technologies, 25030024). In addition, MSC_Pat and hMPCs were supplemented with 2 ng/mL recombinant human FGF (R&D Systems, 233-FB-025). Two days before performing the ChIP experiments, cells were seeded at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.

value: mesenchymal stem cells derived from an EwS patient (MSCPat)

value: WT


title: EWIma5_Tum2_meta_liver


title: EWIma10


title: EWIma6


title: D048T34: MSC_Pat_R1


title: D310T18: MSC_Pat_SPC_cl7_R2


title: D310T17: MSC_Pat_R2


title: D310T20: MSC_Pat_SPC_cl8_R2


title: D211T19: MSC_Pat_SPC_cl8_R1


title: D211T18: MSC_Pat_SPC_cl9_R1


title: D310T19: MSC_Pat_SPC_cl9_R2


title: D211T17: MSC_Pat_SPC_cl7_R1


title: D310T41: EWIma1_siEF1_R2

value: EWSR1-FLI1 low (siEWSR1-FLI1)


title: D310T01: EWIma1_Tumor1


title: D310T40: EWIma1_siEF1_R1


title: D310T38: EWIma1_siCT_R1

value: EWSR1-FLI1 (siCTRL)


title: A945C208: EWIma1_input

data_processing:
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1 and broad forH3K27ac marks. For each cell line, ChIP-seq were normalized according to their respective input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Mesenchymal stem cells derived from an EwS patient

growth_protocol: MSC_Pat and EWIma1 were cultured in aMEM (Life Technologies, 22561021) supplemented with 10% fetal bovine serum (MSC grade, Life Technologies, 12662029) and glutamine at 10mM (Life Technologies, 25030024). In addition, MSC_Pat were supplemented with 2 ng/mL recombinant human FGF (R&D Systems, 233-FB-025). Two days before performing the ChIP experiments, cells were seeded at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.

extract_protocol:
ChiP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For this, MSC_Pat and EWIma1 cell  were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb.
The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

value: SPC mutation + EF1

value: input


title: A945C206: EWIma1_H3K27ac

value: Mesenchymal stem cells derived from an EwS patient


title: A945C207: EWIma1_FLI1


title: D310T39: EWIma1_siCT_R2


title: D310T02: EWIma1_Tumor2


title: D310T04: EWIma1_Tumor4


title: A945C204: MSC_Pat_FLI1


title: D310T03: EWIma1_Tumor3


title: A945C205: MSC_Pat_input


title: D211T05: EWIma1_R3


title: A945C203: MSC_Pat_H3K27ac


title: D211T04: EWIma1_R2


title: D310T37: EWIma1_R5


title: D310T24: hMPC_R2

source_name: mesenchymal precursor cells (hMPCs)

value: mesenchymal precursor cells (hMPCs)


title: D310T21: EWIma1_R4


title: D310T23: hMPC_R3


title: D310T26: hMPC-cl2_STAG2wt_R2


title: D048T35: EWIma1_R1


title: D310T25: hMPC-cl2_STAG2wt_R1


title: D310T27: hMPC-cl2_STAG2wt_R3


title: D310T22: hMPC_R1


title: D310T29: hMPC-cl1_STAG2wt_R2


title: D310T30: hMPC-cl1_STAG2wt_R3


title: D310T34: hMPC-cl2_STAG2KO_R1


title: D310T35: hMPC-cl2_STAG2KO_R2


title: D310T28: hMPC-cl1_STAG2wt_R1


title: D310T33: hMPC-cl1_STAG2KO_R3


title: D310T32: hMPC-cl1_STAG2KO_R2


title: D310T31: hMPC-cl1_STAG2KO_R1


title: S3_T6

status: Public on Aug 13 2021

city: RIVERSIDE

first: Xinru

last: Qiu

address: 109 Picnic Hill Rd

department: School of Medicine

institute: University of California, Riverside

data_processing:
The Cell Ranger software pipeline (v3.1.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the human reference genome (refdata-cellranger-GRCh38-3.0.0) (command cellranger count).
We obtained the feature-barcode matrix that contains gene expression counts in the outputs.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression counts of each individual cell.

source_name: PBMCs from the survived septic patient in the Intensive Care Unit (ICU) at 6 hours from sepsis recognition.

growth_protocol: No growth or treatment performed

extract_protocol:
Human peripheral blood was collected from healthy donors and septic patients. Blood was recovered in Vacutainer glass collection tubes with heparin (BD Biosciences). Peripheral blood mononuclear cells (PBMC) were isolated by gradient centrifugation with Histopaque-1077(400g,30min at room temperature). PBMC cells at the interface of plasma and Histopaque were harvested by paster pipette then washed twice with growth medium (RPMI 1640, 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine). Cell aliquots were frozen in liquid nitrogen with 10%DMSO and 90% FBS. For single cell sequencing, cryovials were thawed in the water bath at 37°C for 2-3 min. In a biosafety hood, thawed cells were transferred to a 50 ml conical tube using a wide-bore pipette tip. Cryovial was rinsed with 10 ml warm complete growth medium. Cell suspension was centrifuged at 300g for 5 min. PBMC live cells were recovered by dead cell removal kit (Miltenyi) and viable cells confirmed by hemocytometer counting (>85% viable). 2 x 106 cells were transferred into a new 50-ml tube and centrifuged at 300g for 5 min. Supernatant was gently removed without disrupting the cell pellet, which was then re-suspended in 1 ml 1X PBS + 0.04% BSA and gently mixed by pipette. Cells were transferred into a 2ml microcentrifuge tube then centrifuged, 300g for 5 min, then supernatant removed without disrupting the cell pellet. Cells were resuspended in an appropriate volume of 1X PBS + 0.04% BSA to obtain a concentration of 700-1,200 cells/μl then placed on ice. 15,000 cells/sample single-cell suspensions were loaded into a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions.
The single-cell RNA-seq libraries for Illumina sequencing using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) was performed according to the manufacturer’s instructions. Samples were sequenced at UCSD Genomics center on the NovaSeq platform at 250M reads/sample.

treatment_protocol: No growth or treatment performed

tag: donor id

value: donor 7

tag: disease state

value: survived septic patient

value: blood

tag: sample name

tag: Sex

value: Female

tag: age range


title: S3_T0

source_name: PBMCs from the survived septic patient in the Intensive Care Unit (ICU) at 0 hours from sepsis recognition.


title: S2_T0

value: donor 6

value: Male


title: NS ES_T0

source_name: PBMCs from the non-survived septic patient in the Intensive Care Unit (ICU) at 0 hours from sepsis recognition.

value: donor 5

value: non-survived septic patient

value: NS ES_T0


title: PDS-IP-rep1

status: Public on Mar 16 2021

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

data_processing:
extract unique molecular identifiers with umi_tools
Trims adapters & adapter-dimers with cutadapt
Maps to repeat elements with STAR and filter
Maps filtered reads to genome with STAR
Removes PCR-duplicates with umi_tools (single-end)
Calls enriched peak regions (peak clusters) with CLIPPER
Uses size-matched input sample to normalize and calculate fold-change enrichment within enriched peak regions with custom perl scripts
IDR analysis is run as a second processing pipeline (merge_peaks) available with additional documentation on github
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain reproducible peaks. Column headers:  chromosome, start, end, geomean of log2 fold change, minimum of the -log10 pvalue between two replicates, strand
Supplementary_files_format_and_content: bigwig files display the dense and continuous data in a genome browser track

source_name: Kidney cells

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, life Technologies) containing 10% fetal bovine serum (Invitrogen) and 1% penicillin and streptomycin (Invitrogen), and the cells were maintained at 37°C in an incubator containing 5% CO2

extract_protocol: seCLIP experiments were performed with an eCLIP Library Prep Kit (Eclipse BioInnovations) following the manufacturer’s instructions

treatment_protocol: HEK293T cells for seCLIP-Seq were either not treated (Ctrl) or treated with 20 μM PDS at 12 h before UVA crosslinking

tag: cell type

value: human embryonic kidney cells

tag: cell line

value: PDS treatment for 12h

tag: clip antibody

value: G3BP1 (MBL International, RN048PW)


title: PDS-Input-rep2

tag: treatment

value: No


title: Ctrl-Input-rep2

value: No treatment


title: Ctrl-IP-rep2


title: Ctrl-IP-rep1


title: D310T36: hMPC-cl2_STAG2KO_R3

value: Mut


title: 1927_ACC_AN

status: Public on Mar 10 2021

data_processing:
Library strategy: ATAC-seq
The obtained sequences were adapter trimmed and aligned to the mouse reference genome (mm10 including small contigs) using the BWA-MEM software (arXiv:1303.3997v1).
We selected and used only uniquely aligned reads for the analysis. Reads aligned to mitochondrial DNA and PCR duplicate reads were eliminated from further analysis.
Peak calling was performed using the MACS2 peak-calling software.
Genome_build: hg38

source_name: FACS-sorted non-neuronal (NeuN-) nuclei

extract_protocol:
100 mg of pulverized anterior cingulate cortex (ACC) tissue was obtained from the NIMH Human Brain Collection Core (HBCC). Total nuclei were  extracted from frozen brain tissue using sucrose gradient centrifugation. Neuronal (NeuN+) and non-neuronal nuclei (NeuN-) were isolated with fluorescence-activated nuclei sorting  using an anti-NeuN antibody conjugated to AlexaFluor-488 on a FACSAria instrument. For a detailed protocol for nuclei isolation, see Kundakovic et al, 2017
ATAC-seq libraries were prepared according to Buenrostro et al. 2013 (PMID:24097267) with some modifications. Illumina Nextera DNA Library Prep kit (FC-121-1030) and Nextera Index kit (FC 121-1011) were used to prepare the libraries.

tag: brain bank tissue source

value: HBCC

tag: individual id

value: anterior cingulate cortex (ACC)

tag: dx

value: control

tag: manner of death

value: natural

tag: gender

value: male

tag: age of death

tag: race

value: African American

tag: height (in)

tag: weight (lb)

tag: post-mortem interval (hours)

tag: ph


title: Ctrl-Input-rep1


title: PDS-Input-rep1


title: HEX_2

data_processing:
Library strategy: ATAC-seq
The obtained sequences were adapter trimmed and aligned to the mouse reference genome (mm10 including small contigs) using the BWA-MEM software (arXiv:1303.3997v1).
We selected and used only uniquely aligned reads for the analysis. Reads aligned to mitochondrial DNA and PCR duplicate reads were eliminated from further analysis.
Read numbers were down-sampled so that peak calling was based on comparable numbers of reads for each sample.
We performed peak calling using MACS2 and calculated the irreproducible discovery rates (IDR) of the detected peaks between biological replicates to select the high confidence peaks (IDR < 0.05).
We selected peaks which were shared across two biological replicates with an IDR <0.05.
Genome_build: mm10

source_name: FACS-sorted neuronal (NeuN+) nuclei

extract_protocol:
Frontal cortex was bilaterally dissected from the brain and frozen in either liquid nitrogen, hexane, or slow-freezing medium. Total nuclei were then extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated from non-neuronal nuclei (NeuN-) with fluorescence-activated nuclei sorting  using an anti-NeuN antibody conjugated to AlexaFluor-488 on a FACSAria instrument. For a detailed protocol for nuclei isolation and purification of neuronal nuclei, see Kundakovic et al, 2017 (PMID:27113501).
ATAC-seq libraries were prepared according to Buenrostro et al. 2013 (PMID:24097267) with some modifications. Illumina Nextera DNA Library Prep kit (FC-121-1030) and Nextera Index kit (FC 121-1011) were used to prepare the libraries.

tag: strain

tag: tissue

value: frontal cortex

tag: age

value: 11 weeks

tag: Sex

tag: freezing condition

value: hexane


title: LN2_2

value: liquid nitrogen


title: 1936_ACC_AP

value: Caucasian


title: MED_1

value: freezing medium


title: 1927_ACC_AP


title: S1 T6

status: Public on Mar 03 2021

tag: donor

value: Tissue donor 4

value: Blood

tag: disease state

value: survived septic patient

tag: sample name

value: S1 T6

value: Female

tag: age range


title: S1 T0

value: S1 T0


title: NS LS T6

source_name: PBMCs from the non-survived septic patient in the Intensive Care Unit (ICU) at 6 hours from sepsis recognition.

value: Tissue donor 3

value: non-survived septic patient

value: NS LS T6

value: Male


title: LN2_1

value: male


title: S2_T6

tag: donor id

value: donor 6

value: blood


title: HC1

source_name: PBMCs from non-sepsis donor 1.

value: Tissue donor 1

value: healthy control


title: HC2

source_name: PBMCs from non-sepsis donor 2.

value: Tissue donor 2


title: NS ES_T6

value: donor 5

value: NS ES_T6


title: PDS-IP-rep2

tag: cell type

value: human embryonic kidney cells

tag: cell line

tag: treatment

value: PDS treatment for 12h

tag: clip antibody

value: G3BP1 (MBL International, RN048PW)


title: Human_skin_fib_rep4

status: Public on Feb 22 2021

city: Singapore

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -p -R -G
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: human dermal fibroblasts from a healthy donor

extract_protocol:
The total RNA of primary human dermal fibroblasts, extracted using the RNeasy mini kit (Qiagen), was quantified using Qubit RNA high sensitivity assay kit (Thermo Fisher Scientific) and RNA integrity number (RIN) was assessed using the LabChip GX RNA Assay Reagent Kit (Perkin Elmer).
Libraries prepared using the TruSeq Stranded mRNA Kit (Illumina) were pooled and sequenced on a NextSeq 500 sequencer (Illumina) using NextSeq 500 High Output v2 kit and paired-end 75–base pair sequencing chemistry.

tag: subject status

value: healthy donor

value: dermal fibroblasts

tag: rin


title: Human_skin_fib_rep2


title: Human_skin_fib_rep3


title: MED_2

value: frontal cortex

value: 11 weeks

value: freezing medium


title: HEX_1

value: hexane


title: cohort-2_53

status: Public on Jan 19 2021

description: DNA methylation

data_processing:
RRBS raw sequencing reads was aligned to hg19 and analyzed through a Streamlined Analysis and Annotation Pipeline (SAAP-RRBS)
Genome_build: hg19

source_name: STS

extract_protocol:
phenol-chloroform
libraries were constructed according to illumina's instructions

value: kidney

tag: disease stage

value: STS


title: cohort-2_54

description: DNA methylation


title: cohort-2_55

description: DNA methylation


title: cohort-2_52

description: DNA methylation


title: cohort-2_56

description: DNA methylation


title: cohort-2_50

description: DNA methylation


title: cohort-2_46

description: DNA methylation


title: cohort-2_51

description: DNA methylation


title: NS LS T0

value: Tissue donor 3

value: Blood

value: non-survived septic patient

value: NS LS T0

value: Male


title: cohort-2_47

description: DNA methylation


title: cohort-2_49

description: DNA methylation


title: cohort-2_43

description: DNA methylation


title: cohort-2_42

description: DNA methylation


title: cohort-2_41

description: DNA methylation


title: cohort-2_39

description: DNA methylation


title: cohort-2_44

description: DNA methylation


title: cohort-2_37

description: DNA methylation


title: cohort-2_38

description: DNA methylation


title: cohort-2_40

description: DNA methylation


title: cohort-2_36

description: DNA methylation


title: cohort-2_33

description: DNA methylation


title: cohort-2_30

description: DNA methylation


title: cohort-2_31

description: DNA methylation


title: cohort-2_34

description: DNA methylation


title: cohort-2_32

description: DNA methylation


title: cohort-2_48

description: DNA methylation


title: cohort-2_29

description: DNA methylation

source_name: LTS

value: LTS


title: cohort-2_28

description: DNA methylation


title: cohort-2_45

description: DNA methylation


title: cohort-2_25

description: DNA methylation


title: cohort-2_26

description: DNA methylation


title: cohort-2_24

description: DNA methylation


title: cohort-2_27

description: DNA methylation


title: cohort-2_22

description: DNA methylation


title: cohort-2_18

description: DNA methylation


title: cohort-2_21

description: DNA methylation


title: cohort-2_17

description: DNA methylation


title: cohort-2_35

description: DNA methylation


title: cohort-2_19

description: DNA methylation


title: cohort-2_20

description: DNA methylation


title: cohort-2_16

description: DNA methylation


title: cohort-2_12

description: DNA methylation


title: cohort-2_23

description: DNA methylation


title: cohort-2_14

description: DNA methylation


title: cohort-2_13

description: DNA methylation


title: cohort-2_10

description: DNA methylation


title: cohort-2_7

description: DNA methylation


title: cohort-2_4

description: DNA methylation


title: cohort-2_11

description: DNA methylation


title: cohort-2_5

description: DNA methylation


title: cohort-2_6

description: DNA methylation


title: cohort-2_9

description: DNA methylation


title: cohort-2_3

description: DNA methylation


title: cohort-2_2

description: DNA methylation


title: cohort-2_1

description: DNA methylation


title: cohort-1_36

description: DNA methylation


title: cohort-1_34

description: DNA methylation


title: cohort-1_35

description: DNA methylation


title: cohort-1_33

description: DNA methylation


title: cohort-2_15

description: DNA methylation


title: cohort-1_31

description: DNA methylation


title: cohort-1_32

description: DNA methylation


title: cohort-1_30

description: DNA methylation


title: cohort-1_27

description: DNA methylation


title: cohort-1_29

description: DNA methylation


title: cohort-1_25

description: DNA methylation


title: cohort-1_24

description: DNA methylation


title: cohort-1_28

description: DNA methylation


title: cohort-1_26

description: DNA methylation


title: cohort-1_23

description: DNA methylation


title: cohort-1_21

description: DNA methylation


title: cohort-2_8

description: DNA methylation


title: cohort-1_20

description: DNA methylation


title: cohort-1_19

description: DNA methylation


title: cohort-1_17

description: DNA methylation


title: cohort-1_18

description: DNA methylation


title: cohort-1_16

description: DNA methylation


title: cohort-1_12

description: DNA methylation


title: cohort-1_15

description: DNA methylation


title: cohort-1_11

description: DNA methylation


title: cohort-1_13

description: DNA methylation


title: cohort-1_8

description: DNA methylation


title: cohort-1_10

description: DNA methylation


title: cohort-1_9

description: DNA methylation


title: cohort-1_5

description: DNA methylation


title: cohort-1_4

description: DNA methylation


title: cohort-1_7

description: DNA methylation


title: cohort-1_6

description: DNA methylation


title: control_02

description: DNA methylation

source_name: CON

value: short term survivor (STS)


title: control_01

description: DNA methylation


title: cohort-1_3

description: DNA methylation


title: cohort-1_2

description: DNA methylation


title: cohort-1_22

description: DNA methylation


title: cohort-1_1

description: DNA methylation


title: PeTa_DMSO_6d_1

status: Public on Sep 04 2020

city: Vienna

first: Anna

middle: Christina

last: Obenauf

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Reads were aligned against the human genome (hg38) with STAR.
Aligned reads in 3'-UTR region of each transcript were counted and collapsed to gene level using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: featureCount output files of 3'-UTR counts.

growth_protocol: Cells were cultured as suspension cells in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin and 50 mg/mL streptomycin.

extract_protocol:
Total RNA isolation from cells was performed with an in-house paramagnetic bead-based purification protocol.
3'UTR sequencing libraries were generated from 500ng total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

treatment_protocol: Cells were treated with the indicated compound for 24h or 6d.

value: PeTa

value: Merkel cell carcinoma cell line

value: DMSO


title: Enteric neurons P21 replicate 2

status: Public on Sep 18 2020

city: Stockholm

first: Ulrika

last: Marklund

state: - If in U.S, Select a State -

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA libraries were sequenced by NovaSeq 6000 platform and NovaSeq 6000 S1 Reagent Kit (100 cycles)
Gene expression dataframe was constructed, using Seurt's Read10X(),  from filtered_gene_bc_matrices outputs from the Cell Ranger version 2.1.1 pipeline (for E15_* and E18_*) and Cell Ranger version 3.0.1 (for P21_*)
The expression data were then normalized with Seurat's SCTransform(), retaining 3000 most variable genes for downstream analysis
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: loom files containing UMI counts as well as cell IDs and feature (genes), text files (for each sample) consisting of barcodes (cell IDs), genes and matrix (UMI counts). The processed data present here were taken from filtered_gene_bc_matrices outputs from the Cell Ranger version 2.1.1 pipeline.

source_name: enteric nervous system

extract_protocol:
Small intestines from five embryos at E15.5, three embryos at E18.5 and four mice at P21 were isolated, dissociated using Dispase/Liberase TH, flow sorted and applied to 10xGenomics Chromium Single Cell Kit Version 2.
RNA libraries were prepared for sequencing using standard Illumina protocols
Single Cell RNA sequencing

tag: strain

value: myenteric plexus


title: ENS cells at E18.5

tag: tissue

value: ENS


title: Enteric neurons P21 replicate 1

data_processing:
RNA libraries were sequenced by NovaSeq 6000 platform and NovaSeq 6000 S1 Reagent Kit (100 cycles)
Gene expression dataframe was constructed, using Seurt's Read10X(),  from filtered_gene_bc_matrices outputs from the Cell Ranger version 2.1.1 pipeline (for E15_* and E18_*) and Cell Ranger version 3.0.1 (for P21_*)
The expression data were then normalized with Seurat's SCTransform(), retaining 3000 most variable genes for downstream analysis
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: loom files containing UMI counts as well as cell IDs and feature (genes), text files (for each sample) consisting of barcodes (cell IDs), genes and matrix (UMI counts). The processed data present here were taken from filtered_gene_bc_matrices outputs from the Cell Ranger version 2.1.1 pipeline.
Supplementary_files_format_and_content: R data object (rds) containing analysis of GSM4504450 as presented in PMID: 33288908.

tag: age


title: PeTa_DMSO_6d_3


title: PeTa_DMSO_24h_3


title: cohort-1_14

city: Rochester

first: Keith

last: Robertson

address: 200 First Street SW, Stabile 12-70

institute: Mayo Clinic

description: DNA methylation


title: PeTa_DMSO_24h_2


title: ENS cells at E15.5


title: PeTa_DMSO_6d_2


title: PeTa_DMSO_24h_1


title: PeTa_100nM_GSK_LSD1_6d_1

tag: drug concentration


title: PeTa_100nM_GSK_LSD1_24h_2


title: PeTa_100nM_GSK_LSD1_24h_3


title: PeTa_100nM_GSK_LSD1_6d_2


title: PeTa_100nM_GSK_LSD1_24h_1


title: GSK_6h-3

data_processing:
library strategy: SLAMseq (Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA)
Reads were aligned against the human genome (hg38) with STAR.
reads were processed using SlamDunk v0.2.4 running the full analysis procedure (slamdunk all) and stringency filter set to 2 (requiring ≥ 2 T>C conversions per read)
For details see: http://t-neumann.github.io/slamdunk/docs.html
Genome_build: hg38
Supplementary_files_format_and_content: TSV table containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics.

treatment_protocol: Cells were pre-treated with GSK-LSD1 inhibitor for 30min and 4SU labeling of newly synthesized transcripts was performed for 60 or 360min.

tag: 4su labeling time before harvest (min)


title: GSK_6h-2


title: GSK_6h-1


title: GSK_1h-3


title: Ctrl_6h-3


title: Ctrl_6h-1


title: Ctrl_6h-2


title: GSK_1h-1


title: GSK_1h-2


title: Ctrl_1h-1


title: PeTa_100nM_GSK_LSD1_6d_3


title: Tsix +/- differentiation day 7 (replicate 2)

status: Public on Jun 25 2020

city: Boston

first: Eric

last: Aeby

state: Massachusetts

address: 185 Cambridge Street

department: Department of Molecular Biology and Department of Genetics

institute: Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School

data_processing:
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using bowtie2 and novoalign
allele specific reads were called by custom script (Pinter et al., 2012)
Metagene analysis was done by deeptools2 (Ramirez et al., 2016) and custom python scripts
Strand-specific PRO-seq coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million with deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (fwd:watson, rev:crick strand) and RPKM normalized

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium or differentiated accordingly

extract_protocol:
Total RNA was isolated using TRIzol extraction,biotin-labeled RNA was enriched using strepatividing pulldown
Library preparation is combined to PROseq experiment (three individual streptavidin enrichment steps) and was performed as described in (Kwak et al. 2013 and Mahat et al. 2016); Strand-specific RNA sequencing, multiplexed

treatment_protocol: Nuclei were isolated, permeabilized for nuclear run-on. Nascent transcripts were labeled with Biotin-11-ATP, Biotin-11-CTP, Biotin-11-GTP, Biotin-11-UTP

tag: genotype

value: Tsix +/-

tag: developmental stage

value: differentiation day 7

tag: Sex

value: female

value: C57BL/6J x CAST/EiJ hybrid