title: P3_D5_C4_x1_24


title: P3_C2_C6_x1_26

status: Public on Jun 15 2020

type: SRA

city: London

first: Marcela

last: Lipovsek

address: 18-20 Newcomen Street - New Hunt's House

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

library_source: transcriptomic

data_processing:
Paired-end read fastq files were demultiplexed, quality controlled using FastQC and trimmed using Trim Galore. Reads were pseudoaligned and quantified using kallisto against a reference transcriptome from Ensembl Release 89 (Gencode Release M17 GRCm38.p6) with sequences corresponding to the ERCC spike-ins and the Cre recombinase and tdT genes added to the index. Transcripts were collapsed into genes using the sumAcrossFeatures function in scater (v1.12.2).
Cell level quality control and cell filtering was performed in scater (v1.12.2). Cells with <1000 genes, <100,000 reads, >75% reads mapping to ERCC spike-ins, >10% reads mapping to mitochondrial genes or low library complexity were discarded from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing kallisto estimated counts or tpm (transcripts per million) collapsed to genes

molecule: polyA RNA

organism: Mus musculus

source_name: Olfactory bulb dopaminergic neuron

growth_protocol: Mice of either gender were used and housed under a 12 h light:dark cycle in an environmentally controlled room with access to water and food ad libitum.

extract_protocol:
For manual sorting of fluorescently labelled dopaminergic neurons we adapted the protocol described in Hempel, et al. 2007.
Sequencing libraries were generated following a modified Smart-Seq2 protocol. Briefly, 1 µl of a 1:2,000,000 dilution of ERCC spike-ins (Invitrogen. Cat. no. 4456740) was added to each sample and mRNA was captured using modified oligo-dT biotinylated beads (Dynabeads – Invitrogen). PCR amplification was performed for 22 cycles. Amplified cDNA was cleaned with a 0.8:1 ratio of Ampure-XP beads (Beckman Coulter). cDNAs were quantified on Qubit using HS DNA reagents (Invitrogen) and selected samples were run on a Bioanalyzer HS DNA chip (Agilent) to evaluate size distribution. For generating the sequencing libraries, individual cDNA samples were normalised to 0.2ng/µl and 1µl was used for one-quarter standard-sized Nextera XT (Illumina) tagmentation reactions, with 12 amplification cycles. Sample indexing was performed using index sets A and D (Illumina). At this point, individual samples were pooled according to their index set. Pooled libraries were cleaned using a 0.6:1 ratio of Ampure beads and quantified on Qubit using HS DNA reagents and with the KAPA Library Quantification Kits for Illumina (Roche). Samples were sequenced on two separate rapid-runs on HiSeq2500 (Illumina), generating 100bp paired-end reads. An additional 5 samples were sequenced on MiSeq (Illumina).

treatment_protocol: 24 hours prior to cell collection, mice were subjected to olfactory sensory deprivation by unilateral naris occlusion. Briefly, mice were anesthetised with isoflurane and a custom made plug, coated in petroleum jelly, was inserted into the right naris. Sham controls were obtained by similarly inserting a plug into the right naris and immediately removing it.

tag: strain

tag: tissue

value: Olfactory bulb

tag: sample type

value: Single cell


title: P3_C1_C4_x1_41


title: P3_C4_C5_x1_47


title: P3_C3_C7_x1_50


title: P3_B9_O2_x1_10


title: P3_B1_O6_x1_38


title: P3_A12_C7_x1_79


title: P3_A10_O5_x0_85

source_name: No_cell control

value: No_cell control


title: P3_A7_O6_x1_17


title: P3_B7_O2_x1_59


title: P3_A8_O5_x1_94


title: P3_A5_O5_x1_72


title: P3_D8_C4_x1_70


title: P2_H11_O3_x1_63


title: P3_D7_O6_x1_8


title: P3_A2_C4_x1_67


title: P3_A3_O3_x1_74


title: P2_H12_C5_x1_22


title: P2_H9_O2_x1_48


title: P2_H8_C4_x1_10


title: P2_H10_C5_x1_17


title: P2_G12_O5_x1_79


title: P2_H4_O4_x1_71


title: P2_H5_O6_x1_82


title: P2_G8_O5_x1_81


title: P2_H7_C7_x1_40


title: P3_B3_O4_x1_7


title: P2_H3_O6_x1_84


title: P2_G11_C3_x1_03


title: P2_H1_C3_x1_02


title: P2_G7_O4_x1_66


title: P2_H6_C6_x1_31


title: P2_G9_O2_x1_54


title: P2_G6_C4_x1_12


title: P2_G3_O3_x1_55


title: P2_G2_C6_x1_33


title: P2_G10_C6_x1_26


title: P2_G5_O2_x0_95


title: P2_G1_C6_x1_29


title: P2_G4_C5_x1_23


title: P2_F11_O2_Neg_96

source_name: Negative control

value: Negative control


title: P2_F12_O6_x1_86


title: P2_F7_O2_x1_52


title: P2_F9_C6_x1_34


title: P2_F10_O5_x1_76


title: P2_F8_O2_x10_93

source_name: Positive control

value: Positive control


title: P2_H2_O6_x1_90


title: P2_F3_C4_x1_13


title: P2_F2_O6_x1_89


title: P2_E12_C7_x1_42


title: P2_E10_C6_x1_24


title: P2_E11_O4_x1_69


title: P2_E8_O5_x1_73


title: P2_E9_O3_x1_56


title: P2_E3_C4_x1_08


title: P2_E6_O2_x1_47


title: P2_F1_C6_x1_35


title: P2_E4_C6_x1_25


title: P2_D11_C7_x1_43


title: P2_E1_O4_x1_67


title: P2_D8_C6_x0_94


title: P2_F6_C6_x1_27


title: P2_D12_O6_x1_85


title: P2_E7_C7_x1_44


title: P2_E2_O2_x1_50


title: P2_D7_O4_x1_68


title: P2_D9_O3_x1_60


title: P2_D5_O4_x1_65


title: P2_D4_O6_x1_83


title: P2_D6_O4_x1_64


title: P2_D10_O5_x1_80


title: P2_F5_O3_x1_57


title: P2_F4_O4_x1_72


title: P2_D3_C5_x1_16


title: P2_D2_O2_x1_51


title: P2_D1_C7_x1_36


title: P2_C12_O3_x1_62


title: P2_E5_C6_x10_91


title: P2_C11_O6_x1_87


title: P2_C10_C5_x1_18


title: P2_C6_C5_x1_15


title: P2_C5_C3_x1_06


title: P2_C7_O5_x1_78


title: P2_C9_O5_x1_77


title: P2_C4_C7_x10_92


title: P2_C2_C5_x1_20


title: P2_C8_O5_x1_75


title: P2_C3_C4_x1_14


title: P2_B10_C6_x1_32


title: P2_B5_O2_x1_46


title: P2_B6_C7_x1_45


title: P2_B8_C3_x1_05


title: P2_C1_C7_x1_37


title: P2_B9_O2_x1_53


title: P2_B3_O3_x1_61


title: P2_B4_C6_x1_28


title: P2_B2_O3_x1_58


title: P2_A9_O5_x1_74


title: P2_A11_C4_x1_07


title: P2_B11_C3_x1_01


title: P2_B12_C4_x1_11


title: P2_A10_O6_x1_88


title: P2_B1_C4_x1_09


title: P2_A12_C7_x1_38


title: P2_A8_C7_x1_39


title: P2_A7_O4_x1_70


title: P2_A6_C7_x1_41


title: P2_A5_C6_x1_30


title: P2_A4_C5_x1_19


title: P2_A3_O2_x1_49


title: P2_A2_C3_x1_04


title: P2_A1_O3_x1_59


title: P2_B7_C5_x1_21


title: P1_H12_C7_x10_92


title: P1_H11_O2_x0_95


title: P1_H9_O6_x1_84


title: P1_H7_C3_x1_06


title: P1_H3_O2_x1_51


title: P1_H4_O2_x1_50


title: P1_H5_C4_x1_08


title: P1_H6_C5_x1_15


title: P1_H10_C7_x1_42


title: P1_H8_O4_x1_64


title: P1_G12_O6_x1_83


title: P1_G9_O3_x1_61


title: P1_G11_C5_x1_17


title: P1_G7_C3_x1_05


title: P1_H2_O2_Neg_96


title: P1_G6_C6_x0_94


title: P1_H1_C3_x1_03


title: P1_G4_C6_x1_34


title: P1_G3_C7_x1_44


title: P1_G2_C6_x1_27


title: P1_F12_C6_x1_32


title: P1_G1_O5_x1_76


title: P1_F11_C3_x1_02


title: P1_F7_C5_x1_23


title: P1_F10_O2_x1_49


title: P1_F6_O5_x1_81


title: P1_F5_C6_x1_33


title: P1_G8_C6_x1_29


title: P1_G10_O2_x1_47


title: P1_F3_C7_x1_43


title: P1_G5_C3_x1_04


title: P1_F2_O2_x1_54


title: P1_E12_O2_x1_52


title: P1_F4_O4_x1_67


title: P1_E7_C7_x1_45


title: P1_E6_O5_x1_78


title: P1_E5_C7_x1_38


title: P1_E11_O3_x1_63


title: P1_E3_O6_x1_85


title: P1_E4_O3_x1_56


title: P1_E10_O2_x1_46


title: P1_F1_C6_x1_25


title: P1_E1_O5_x1_79


title: P1_E8_O3_x1_60


title: P1_D12_O2_x10_93


title: P1_E2_C5_x1_21


title: P1_D11_O5_x1_77


title: P1_F9_C4_x1_12


title: P1_D9_O4_x1_71


title: P1_F8_C6_x1_31


title: P1_D8_C7_x1_39


title: P1_D5_O6_x1_87


title: P1_D6_C4_x1_10


title: P1_D7_O4_x1_69


title: P1_E9_C6_x1_35


title: P1_D4_C4_x1_14


title: P1_D3_C6_x1_28


title: P1_D1_O6_x1_90


title: P1_D2_C4_x1_07


title: P1_C12_O2_x1_53


title: P1_C10_O6_x1_88


title: P1_C9_C4_x1_13


title: P1_C11_O3_x1_55


title: P1_C8_C5_x1_20


title: P1_C5_O3_x1_58


title: P1_C6_O4_x1_65


title: P1_D10_C5_x1_18


title: P1_C4_O2_x1_48


title: P1_B9_C7_x1_36


title: P1_C7_O4_x1_72


title: P1_B5_O3_x1_59


title: P1_B8_O5_x1_80


title: P1_B10_O4_x1_66


title: P1_B12_C4_x1_09


title: P1_C3_O3_x1_62


title: P1_B11_C3_x1_01


title: P1_B7_C4_x1_11


title: P1_B6_O5_x1_74


title: P1_B4_C5_x1_16


title: P1_B3_O6_x1_89


title: P1_B2_O5_x1_73


title: P1_B1_C7_x1_40


title: P1_A12_C6_x1_26


title: P1_A11_C5_x1_19


title: P1_A10_O4_x1_68


title: P1_A8_O5_x1_75


title: P1_A7_C7_x1_41


title: P1_A9_O6_x1_82


title: P1_C1_O6_x1_86


title: P1_A6_O3_x1_57


title: P1_A3_O4_x1_70


title: P1_C2_C7_x1_37


title: P1_A2_C5_x1_22


title: P1_A1_C6_x1_24


title: ChIPseq, ES_RepB, input

city: hopkinton

first: barry

middle: A

last: kesner

state: ma

address: 1 chamberlain street

country: USA

institute: molecular biology

library_source: genomic

data_processing:
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates. Sequencing depth between libraries was normalized to the least-sequenced library based on the number of uniquely mapped reads to autosomes by random down-sampling using samtools. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, genes with insufficient allelic information (<13 allele-specific reads) or expressed at low level (less than 1 RPKM in all samples) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts/total counts) applied to comp RPKM.
Genome_build: mm9
ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.

molecule: genomic DNA

growth_protocol: ES cells were grown on γ-irradiated MEF feeders for 3 days prior to differentiation in ES medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX, LIF) with 15% FBS. For differentiation, ES colonies were trypsinized and feeders removed. ES cells were allowed to differentiate in suspension, forming embryoid bodies (EBs), for 4 days in differentiation medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 15% FBS. EBs were settled down on gelatin-coated plates at day 4 and allowed to further differentiate for 10 days until harvesting.

extract_protocol:
ChIP-seq: Cells were crosslinked with 1% formaldehyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Lysates were precleared for 1 hour, then 10% saved as input, and incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromatin was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
RNA-seq: Total cell RNA was extracted using TRIzol (Thermo Fisher), from which mRNA was isolated using oligo(dT) beads and RNA-seq libraries prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 9-14 cycles of PCR amplification, depending on library concentration measured by qPCR.

value: CAST/Ei x 129/Sv/Jae

tag: cell type

value: ES cell

tag: genotype

value: RepB

tag: antibody


title: ChIPseq, MEF_RepA, input

data_processing:
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates. Sequencing depth between libraries was normalized to the least-sequenced library based on the number of uniquely mapped reads to autosomes by random down-sampling using samtools. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, genes with insufficient allelic information (<13 allele-specific reads) or expressed at low level (less than 1 RPKM in all samples) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts/total counts) applied to comp RPKM.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.

value: MEF cell

value: RepA


title: ChIPseq, ES_RepB, Day14, H3K27me3

tag: time point


title: ChIPseq, MEF_RepA, H2AK119ub

value: H2AK119ub(Cell Signaling Technology, 8240, lot 2)


title: ChIPseq, MEF_RepA, H3K27me3


title: ChIPseq, ES_WT, input

value: wildtype


title: ChIPseq, ES_RepB, Day5, H2AK119ub


title: ChIPseq, ES_RepB, Day0, H3K27me3


title: ChIPseq, ES_RepB, Day14, H2AK119ub


title: ChIPseq, ES_RepB, Day0, H2AK119ub


title: ChIPseq, ES_WT, Day8, H3K27me3


title: ChIPseq, ES_RepB, Day5, H3K27me3


title: ChIPseq, ES_WT, Day0, H3K27me3


title: P1_A4_C6_x10_91


title: ChIPseq, ES_WT, Day5, H3K27me3


title: ChIPseq, ES_WT, Day8, H2AK119ub


title: ChIPseq, ES_WT, Day5, H2AK119ub


title: RNAseq, ES_RepB, Day10


title: RNAseq, ES_RepB, Day8


title: ChIPseq, ES_WT, Day0, H2AK119ub


title: RNAseq, ES_RepB, Day7


title: ChIPseq, ES_RepB, Day8, H3K27me3


title: P1_A5_C6_x1_30


title: RNAseq, ES_RepB, Day5


title: ChIPseq, ES_WT, Day14, H3K27me3


title: RNAseq, ES_RepB, Day6


title: RNAseq, ES_RepB, Day0


title: ChIPseq, ES_RepB, Day8, H2AK119ub


title: RNAseq, ES_WT, Day8


title: RNAseq, ES_WT, Day5


title: RNAseq, ES_WT, Day7


title: RNAseq, ES_WT, Day10


title: RNAseq, ES_WT, Day6


title: 5mC Tet2-KO

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

country: China

institute: Tongji University

description: MeDIP

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using Bowtie2(v2.2.3) default commands.
Peaks were called using masc2(v 2.1.1.20160309) with the parameters "macs2 callpeak -g mm -n $1 -B -q 0.05 --SPMR" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: MeDIP of Tet2-KO mTSCs cell line 2

growth_protocol: TSCs were cultured on 70% FCM+25 ng/ml F4H (25 ng/ml fibroblast growth factor 4 (FGF4); Peprotech and 1.0 μg/ml heparin; Sigma). For the in vitro differentiation of mTSCs, mTSCs were separately plated onto 35mm tissue culture dishes with TSC medium without F4H for up to 7 days with medium changed every day.

extract_protocol:
Total RNA was isolated from cell pellets by Trizol reagent and genomic DNA was prepared using a Genomic DNA Purification Kit (Promega)
RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer’s recommendations (Cat No. KK8440 box1 and KK8420 box2). Briefly, the mRNA was enriched using oligo(dT) magnetic beads and sheared to create short fragments of approximately 300 bp. cDNA was synthesized using random hexamer primers and purified using 1.8X Agencourt AMPure XP beads (Beckman). Finally, the sequencing primers linked to the cDNA fragments (approximately 300 bp) were isolated by gel electrophoresis and enriched by PCR amplification to construct the library. The sequencing was performed at the Sequencing Center in National Institute of Biology, Beijing using the HiSeq 2500 system developed by Illumina. Paired-end 100-bp sequencing was applied. For (h)MeDIP-seq, 3 μg of genomic DNA was used to prepare the sample for sonicated fragmentation. After sonication of genomic DNA the ends of the DNA fragments were repaired and paired-end sequencing specific adaptors (Illumina) were ligated using either a Paired-End DNA Sample Preparation Kit (Illumina) or NEBNext DNA Sample Prep Reagent Set 1 (NEB). Following adaptor ligation, 1/50 of each sample was saved as input, the other DNA was immunoprecipitated and purified. Fragments were amplified with 12–18 cycles using adaptor specific primers (Illumina); fragments ranging between 200 and 500 bp in size were gel-purified before cluster generation and sequencing.

tag: genotype/variation


title: Tet2-KO input

description: MeDIP

source_name: input of Tet2-KO mTSCs cell line 2


title: WT input

description: MeDIP

source_name: input P of WT mTSCs cell line RO-7

value: WT


title: 5hmC Tet2-KO

description: hMeDIP

source_name: hMeDIP of Tet2-KO mTSCs cell line 2


title: ChIPseq, ES_WT, Day14, H2AK119ub


title: 5hmC WT

description: hMeDIP

source_name: hMeDIP of WT mTSCs cell line RO-7


title: Tet2-KO DIF7 rep2

description: RNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using tophat(v1.3.3) default commands.
Differential gene expression was detemined using R package edgeR,genes with absolute value of log2 fold change less than 1 or p-value more than 0.05 were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files and Counts files of gene were generated using cufflinks(v1.2.0) and htseq-count(v0.6.0) default commands

molecule: total RNA

source_name: RNA-seq of differentiated Tet2-KO mTSCs cell line2 at day7


title: RNAseq, ES_WT, Day0


title: 5mC WT

description: MeDIP

source_name: MeDIP of WT mTSCs cell line RO-7


title: WT DIF7 rep1

description: RNA-seq

source_name: RNA-seq of differentiated WT mTSCs at day7


title: Tet2-KO DIF7 rep1

description: RNA-seq


title: WT DIF7 rep2

description: RNA-seq


title: MiSeq_S10


title: MiSeq_S4


title: Macrophages LPS rep2

type: RNA

city: Glasgow

first: Ruaidhri

last: Carmody

address: Sir Graeme Davies Building, 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

description: macrophages derived from bone marrow in vitro

hyb_protocol: Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).

data_processing: Gene expression analysis was performed on Agilent 8x60k mouse arrays (Agilent-028005). All data processing was carried out using Bioconductor packages (Genome Biol. 2004; 5(10): R80) in the R software environment. The data was background corrected using Limma package (Stat Appl Genet Mol Biol. 2004;3). The data was then corrected for batch effects using the ComBat script (Biostatistics. 2007 Jan;8(1):118-27). The corrected data was then normalised between arrays using quantile normalisation (Stat Appl Genet Mol Biol. 2004;3)

source_name: Bone marrow derived macrophages LPS treated 4 hours

label_protocol: Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturerâ€™s protocol.

growth_protocol: Bone marrow derived macrophages were isolated from female 6 - 8 week C57BL/6 mice and differentiated for 7 days in L929 conditioned growth medium.

extract_protocol: Total RNA was extracted using Rneasy mini kit in combination with Qiashredders and a DNase step according to the manufacturers instructions (Qiagen).

treatment_protocol: Cells were treated with a final concentration of 100ng/ul LPS for 4 hours. Cells receiving UPS7 inhibitor were treated with 10µM HBX41,108 for 30 minutes prior to LPS treatment.

value: wild type

tag: treatment

value: LPS treated 4 hours

tag: gender

value: female

value: bone marrow


title: MiSeq_SPos

value: Olfactory bulb


title: MiSeq_SNeg


title: Macrophages untreated rep2

scan_protocol: Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).

source_name: Bone marrow derived macrophages untreated

value: untreated


title: Macrophages LPS+inhibitor rep1

source_name: Bone marrow derived macrophages plus inhibitor LPS treated 4 hours

value: plus inhibitor LPS treated 4 hours


title: MiSeq_SERCC

value: Negative control


title: PP fetus 22 weeks, biological rep 3

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: Gene expression data from freshly isolated fetal liver primary cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on 2.0 Human gene GeneChips arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Expression Console 1.3.1.187 was used for RMA full gene analysis

label: biotin

organism: Homo sapiens

source_name: 2nd trimester fetal liver (17 to 22 weeks)

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix WT plus labeling kit protocol from 0.5 ug total RNA.

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

value: Liver

value: Normal

tag: age

value: 22 weeks gestation


title: ATCC # PCS-100-010, experimental rep1

description: Gene expression data from umbilical vein endothelial cells

source_name: Umblical Vein Endothelial Cells

value: Umblical Vein Endothelial Cells

value: Neonatal


title: P3-3 fetus 22 weeks, biological rep 3

description: Gene expression data from culture of fetal liver primary cells after 2 or 3 passages


title: Macrophages LPS rep1


title: Macrophages LPS+inhibitor rep2


title: PO fetus 17 weeks, biological rep 1

description: Gene expression data from culture of fetal liver primary cells

value: 17 weeks gestation


title: ATCC # PCS-100-010, experimental rep2


title: P2-2 fetus 20 weeks, biological rep 2

value: 20 weeks gestation


title: PO fetus 22 weeks, biological rep 3


title: P2-1 fetus 17 weeks, biological rep 1


title: Macrophages untreated rep1


title: PO fetus 20 weeks, biological rep 2


title: ATCC # PCS-100-010, experimental rep3


title: PP fetus 20 weeks, biological rep 2


title: MiSeq_S8

source_name: Olfactory bulb dopaminergic neuron

value: Single cell


title: MiSeq_S9


title: MiSeq_S1


title: siUPF2 cyto rep1

city: EDINBURGH

first: Kathryn

middle: Alexandra

last: Jackson-Jones

address: Institute of Genetics and Molecular Medicine, Crewe Road South

department: MRC Human Genetics Unit

institute: University of Edinburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg38 whole genome using STAR v2.5.1b with default parameters
The overlap of reads with annotation genes was counted using HTSeq-count v0.9.1 and parameters -s no -m intersection-nonempty
Differential gene expression was analysed using DESeq2 v1.14.1
To stratify membrane-associated and non-membrane genes, gene expression in both fractions in control cells was compared by applying variant stabilised transformation of tpm using DESeq2 v1.14.1, averaged across replicates. Membrane-associated genes were defined as those >2-fold higher expression in membrane fraction than cytoplasmic fraction, all other genes were termed non-membrane.
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-count output: tab-delimited text files for each sample with RPKM values for each gene.

source_name: HeLa cells

extract_protocol:
Cellular fractionation was performed following Jagannathan et al., 2011 with some modifications. Briefly, four days after the first depletion, cells were detached and resuspended in permeabilization buffer (110mM KOAc, 25mM K-HEPES pH 7. 2, 2.5mM Mg(OAc)2, 1mM EGTA, 0.015% digitonin, 1mM DTT, 1× Complete Protease Inhibitor Cocktail, 40U/mL RNaseOUT™) and incubated for 5 minutes on a rotating wheel at 4°C. The resulting cytosolic fractions were recovered by centrifugation at 2000g for 10 minutes, 4°C. The cells were then lysed in NP-40 lysis buffer (400mM KOAc, 25mM K-HEPES pH 7.2, 15mM Mg(OAc)2, 1% (v/v) NP-40, 1mM DTT, 1× Complete Protease Inhibitor Cocktail, 40U/mL RNaseOut) for 30 minutes on ice. Membrane fraction was recovered by centrifugation at 7000g  for 10 minutes at 4°C. Both cytosolic and membrane fractions were clarified by centrifugation. RNA from both fractions was isolated using PureLink RNA Mini Kit (Life Technologies) according to manufacturer’s instructions. DNA was removed using TURBO DNA-free™ DNase I kit (Invitrogen Ambion; AM1907).#
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were double depleted with siRNA pool against UPF1 or NBAS, or si-scr control

tag: cell line

value: HeLa

tag: rna fraction

value: cytoplasm

tag: knockdown


title: siUPF2 mem rep2

value: membrane


title: siUPF2 mem rep3


title: siUPF2 mem rep1


title: siUPF2 cyto rep2


title: siUPF2 cyto rep3


title: siNBAS mem rep3

description: siNBAS

value: siNBAS


title: siNBAS cyto rep3

description: siNBAS


title: siUPF1 mem rep3


title: siUPF1 mem rep1


title: siUPF1 cyto rep3


title: siUPF1 cyto rep2


title: siNBAS cyto rep2

description: siNBAS


title: siUPF1 cyto rep1


title: siNBAS cyto rep1

description: siNBAS


title: siScr mem rep2

description: si-scr control

value: si-scr control


title: siScr mem rep1

description: si-scr control


title: siScr mem rep3

description: si-scr control


title: siScr cyto rep2

description: si-scr control


title: EC Patient 12 RNAseq Total CD4 T cells

city: Cambridge

first: Ce

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline. STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv, summits in BED

source_name: Total CD4 T cells

growth_protocol: Ex vivo PBMC from different patient cohorts were directed sorted and used for NGS.

extract_protocol:
Total RNA was extracted using a commercial PicoPure RNA Isolation Kit
Whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 550 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the GRCh38 human genome database.

treatment_protocol: There is no treatment for patient samples.

tag: patient

value: EC Patient 12

value: peripheral blood

tag: replicate

value: Total CD4 T cells


title: EC Patient 12 RNAseq Effector memory CD4 T cells

source_name: Effector memory CD4 T cells

value: Effector memory CD4 T cells


title: siUPF1 mem rep2


title: siNBAS mem rep1

description: siNBAS


title: siNBAS mem rep2

description: siNBAS


title: EC Patient 11 RNAseq Naive CD4 T cells

source_name: Naive CD4 T cells

value: EC Patient 11

value: Naive CD4 T cells


title: EC Patient 11 RNAseq TEMRA CD4 T cells

source_name: TEMRA CD4 T cells

value: TEMRA CD4 T cells


title: EC Patient 11 RNAseq Effector memory CD4 T cells


title: EC Patient 10 RNAseq Total CD4 T cells

value: EC Patient 10


title: siScr cyto rep3

description: si-scr control


title: EC Patient 09 RNAseq Total CD4 T cells

value: EC Patient 09


title: EC Patient 09 RNAseq TEMRA CD4 T cells


title: EC Patient 12 RNAseq TEMRA CD4 T cells


title: EC Patient 10 RNAseq Effector memory CD4 T cells


title: EC Patient 09 RNAseq Naive CD4 T cells


title: PP fetus 17 weeks, biological rep 1

value: Liver

value: Normal

value: 17 weeks gestation


title: EC Patient 08 RNAseq Naive CD4 T cells

value: EC Patient 08


title: EC Patient 08 RNAseq Total CD4 T cells


title: EC Patient 12 RNAseq Central memory CD4 T cells

source_name: Central memory CD4 T cells

value: Central memory CD4 T cells


title: EC Patient 08 RNAseq Central memory CD4 T cells


title: EC Patient 12 RNAseq Naive CD4 T cells


title: EC Patient 09 RNAseq Effector memory CD4 T cells


title: EC Patient 11 RNAseq Total CD4 T cells


title: EC Patient 06 RNAseq Total CD4 T cells

value: EC Patient 06


title: EC Patient 05 RNAseq TEMRA CD4 T cells

value: EC Patient 05


title: EC Patient 06 RNAseq Central memory CD4 T cells


title: EC Patient 05 RNAseq Naive CD4 T cells


title: EC Patient 11 RNAseq Central memory CD4 T cells


title: siScr cyto rep1

description: si-scr control

value: HeLa

value: cytoplasm

value: si-scr control


title: EC Patient 04 RNAseq Total CD4 T cells

value: EC Patient 04

value: peripheral blood

value: Total CD4 T cells


title: EC Patient 10 RNAseq TEMRA CD4 T cells


title: EC Patient 04 RNAseq Naive CD4 T cells

value: Naive CD4 T cells


title: EC Patient 05 RNAseq Central memory CD4 T cells


title: EC Patient 10 RNAseq Naive CD4 T cells


title: EC Patient 04 RNAseq Central memory CD4 T cells


title: EC Patient 10 RNAseq Central memory CD4 T cells


title: EC Patient 07 RNAseq Central memory CD4 T cells

value: EC Patient 07


title: EC Patient 09 RNAseq Central memory CD4 T cells


title: EC Patient 03 RNAseq Total CD4 T cells

value: EC Patient 03


title: EC Patient 08 RNAseq TEMRA CD4 T cells

value: TEMRA CD4 T cells


title: EC Patient 03 RNAseq Central memory CD4 T cells


title: EC Patient 03 RNAseq Effector memory CD4 T cells

value: Effector memory CD4 T cells


title: EC Patient 07 RNAseq Total CD4 T cells


title: EC Patient 07 RNAseq TEMRA CD4 T cells


title: EC Patient 02 RNAseq Total CD4 T cells

value: EC Patient 02


title: EC Patient 02 RNAseq TEMRA CD4 T cells


title: EC Patient 02 RNAseq Central memory CD4 T cells


title: EC Patient 02 RNAseq Effector memory CD4 T cells


title: EC Patient 07 RNAseq Naive CD4 T cells


title: EC Patient 01 RNAseq Effector memory CD4 T cells

value: EC Patient 01


title: EC Patient 01 RNAseq Naive CD4 T cells


title: EC Patient 07 RNAseq Effector memory CD4 T cells


title: ART Patient 03 RNAseq Total CD4 T cells

value: ART Patient 03


title: Larval wing disc cells, enGFP

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS
Single-read 50 bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.
Reads were aligned using Tophat2 v2.0.12
RPKM expression values from different conditions were extracted and compared by cuffdiff v2.2.1 using Refseq gene models [2].
Genome_build: dm6 Drosophila
Supplementary_files_format_and_content: RPKMs

organism: Drosophila melanogaster

source_name: Larval wing disc cells

growth_protocol: Drosophila of the relevant genotypes were cultured under standard conditions at 25 degrees Celsius in humidity-controlled incubators with 12hr light:dark cycles

extract_protocol:
Wandering stage (L3 instar) larvae were sorted for GFP expression under a dissecting microscope equipped with a Zeiss HBO lamp and a GFP filter. Larvae were rinsed in 1x PBS and then dissected to remove wing discs, which were then immediately dissolved in Trizol (TM) kept on ice. Disc+Trizol mixtures from one 2hr dissection session were frozen at -80 degrees Celsius. This was repeated until 80-100 total discs per genotype (en>GFP or en>GFP,Tai) had been collected. Discs were then pooled within genotypes, and total RNA was extracted according the manufacturer's instructions and depleted for rRNA prior to analysis.
4 µg of total RNA was rRNA depleted and utilized for library construction with the Illumina TruSeq RNA Sample Preparation Kit v2 following the manufacturer's instructions. Libraries were sequenced with an Illumina HiScan platform.

value: GFP+

value: Larval wing disc cells


title: EC Patient 06 RNAseq Naive CD4 T cells

value: EC Patient 06


title: ART Patient 03 RNAseq Naive CD4 T cells


title: EC Patient 06 RNAseq TEMRA CD4 T cells


title: EC Patient 06 RNAseq Effector memory CD4 T cells


title: ART Patient 03 RNAseq Central memory CD4 T cells

value: Central memory CD4 T cells


title: EC Patient 05 RNAseq Total CD4 T cells

value: EC Patient 05


title: EC Patient 08 RNAseq Effector memory CD4 T cells

value: EC Patient 08


title: ART Patient 02 RNAseq TEMRA CD4 T cells

value: ART Patient 02


title: DLD-1_AID-NeonGreen-TPR_LeptomycinB_2hr_replicate3

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

description: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Leptomycin B for 2hr replicate3

data_processing:
We used CASAVA 1.8.2 for the base calling (Illumina, San Diego, CA).
We used STAR aligner version 2.6.1c (Dobin et al., 2013, PMID: 23104886) with the default parameters to map RNA-Seq reads to human reference genome (GRCh38, obtained from Ensembl.org).
We counted the short-reads at the gene level using featureCounts 1.5.2 (Liao et al., 2014, PMID: 24227677). We used "-O" (allowMultiOverlap) and "-p" (isPairedEnd) parameters.
Genome_build: Human reference genome GRCh38 (obtained from Ensembl.org, release 87).
Supplementary_files_format_and_content: Tab-limited text files have human gene IDs (Ensembl 87) as well as read counts from featureCounts.

source_name: DLD-1 cells

growth_protocol: The human colorectal cancer cell line DLD-1 was cultured in DMEM supplemented with heat-inactivated 10% FBS, antibiotics, and 2 mM GlutaMAX in 5% CO2 atmosphere at 37°C. From 75 to 100K of AID-tagged cells were plated on each well of 6-well plate dishes for RNA isolation. Cells at 85% of confluency were washed with PBS and lysed with RLT buffer.

extract_protocol:
RNAeasy Mini Kit (Qiagen). Extracted RNA was analyzed for 260/280 and RIN value on Bioanalyzer 2100 (Agilent).
TruSeq Standard Total RNA Library Prep Kit (Illumina, San Diego, CA) was used to generate RNA-Seq libraries for the Illumina-platforms. The libraries were prepared by the Molecular Genomics Core at the Eunice Kennedy Shriver National Institutes of Child Health and Human Development (Bethesda, MD) as per manufacture’s guideline using Ribo-Zero Gold.

treatment_protocol: All AID-tagged cell lines were treated with 1 mM auxin (I5148, Sigma Aldrich) for Tpr nucleoporin loss for 2 hours

value: AID-NeonGreen-TPR

tag: treatments

value: Leptomycin B

tag: incubation time


title: EC Patient 05 RNAseq Effector memory CD4 T cells

tag: tissue

value: peripheral blood


title: EC Patient 04 RNAseq Effector memory CD4 T cells

value: EC Patient 04


title: EC Patient 04 RNAseq TEMRA CD4 T cells


title: EC Patient 03 RNAseq Naive CD4 T cells

value: EC Patient 03

value: Naive CD4 T cells


title: DLD-1_AID-NeonGreen-TPR_LeptomycinB.Auxin_2hr_replicate1

description: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Leptomycin B & Auxin for 2hr replicate1

value: Leptomycin B & Auxin

value: 3hr total LMB, 1h before auxin plus 2 h with auxin


title: DLD-1 cells transfected with RanGAP1-WT-FLAG Replicate 3

description: Replicate 3

data_processing:
CASAVA version 1.8.2 (Illumina, San Diego, CA) was used for the base calling
For mapping of the short reads, STAR aligner version 2.6.1 was used (Dobin et al., 2013, PMID: 23104886) with the default parameters.
We quantified gene-level read counts using featureCounts version 1.6.3 (Liao et al., 2014, PMID: 24227677) with "-O" (allowMultiOverlap) and "-p" (isPairedEnd) parameters, but otherwise default.
Genome_build: Human reference genome GRCh38 (Ensembl release 87)
Supplementary_files_format_and_content: Tab-limited text files that contain Ensembl gene IDs and read counts.

growth_protocol: DLD-1 human colorectal adenocarcinoma cells were maintained in DMEM containing 10% heat-inactivated fetal bovine serum, 50 ug/mL penicillin, 50 ug/mL streptomycin, and 2 mM GlutaMAX at 37°C in a 5% CO2 incubator. 75,000 to 100,000 cells were seeded on 6-well plates. Cells at 85% of confluency were harvested, washed with PBS, and lysed with RLT buffer for RNA extraction.

extract_protocol:
RNAeasy Mini Kit (Qiagen) was used for RNA extraction. A 260/280 ratio was then measured by NanoDrop Spetrophotometer (Thermo Scientific).
The library preparation and sequencing were performed at the Molecular Genomics Core at the Eunice Kennedy Shriver National Institutes of Child Health and Human Development (Bethesda, MD).  The standard TruSeq total RNA library preparation kit was used (Illumina, San Diego, CA).

treatment_protocol: Cell lines were harvested after 0hr, 2 or 3 hrs, or 8 or 10 hrs treatment of 1 mM auxin (I5148, Sigma Aldrich)

tag: developmental stage

value: cell line


title: ART Patient 02 RNAseq Central memory CD4 T cells

tag: cell type


title: DLD-1 cells transfected with RanGAP1-WT-FLAG Replicate 2

description: Replicate 2

tag: genotype


title: ART Patient 01 RNAseq TEMRA CD4 T cells

value: ART Patient 01

value: TEMRA CD4 T cells


title: EC Patient 01 RNAseq Total CD4 T cells

value: EC Patient 01

value: Total CD4 T cells


title: DLD-1 cells transfected with RanGAP1-KR-FLAG Replicate 3

description: Replicate 3


title: EC Patient 02 RNAseq Naive CD4 T cells

value: EC Patient 02


title: EC Patient 01 RNAseq Central memory CD4 T cells

value: Central memory CD4 T cells


title: EC Patient 01 RNAseq TEMRA CD4 T cells


title: DLD-1 cells transfected with RanGAP1-KR-FLAG Replicate 2

description: Replicate 2


title: ART Patient 01 RNAseq Effector memory CD4 T cells

value: Effector memory CD4 T cells


title: Larval wing disc cells, enGFP+Tai

value: Tai+/GFP+

value: Larval wing disc cells


title: DLD-1_AID-NeonGreen-TPR_LeptomycinB.Auxin_2hr_replicate3

description: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Leptomycin B & Auxin for 2hr replicate3

value: AID-NeonGreen-TPR


title: EC Patient 03 RNAseq TEMRA CD4 T cells

value: peripheral blood


title: ART Patient 03 RNAseq TEMRA CD4 T cells

value: ART Patient 03


title: ART Patient 03 RNAseq Effector memory CD4 T cells


title: DLD-1 cells transfected with AID-RanBP2 Replicate 2

description: Replicate 2


title: ART Patient 02 RNAseq Naive CD4 T cells

value: ART Patient 02


title: DLD-1_AID-NeonGreen-TPR_LeptomycinB.Auxin_2hr_replicate2

description: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Leptomycin B & Auxin for 2hr replicate2


title: DLD-1 cells transfected with AID-RanBP2 Replicate 1

description: Replicate 1


title: DLD-1_AID-NeonGreen-TPR_LeptomycinB_2hr_replicate1

description: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Leptomycin B for 2hr replicate1

value: Leptomycin B


title: EC Patient 12 ATACseq Naive CD4 T cells (1)

data_processing:
Reads were trimmed for adaptor sequence, then mapped to GRCh38 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using MACS2. For duplicated samples, peaks were merge using Bioconductor.
Genome_build: GRCh38
Supplementary_files_format_and_content: summits in BED

extract_protocol:
DNA was treated with Tn5 and purified using Chip dna clean & concentrator
20,000 sorted cells were centrifuged at 1500 rpm for 10 min at 4°C in a pre-cooled fixed-angle centrifuge. All supernatant was removed and a modified transposase mixture (including 25 µl of 2x TD buffer, 1.5 µl of TDE1, 0.5 µl of 1% digitonin, 16.5 µl of PBS, 6.5 µl of nuclease-free water) was added to the cells and incubated in a heat block at 37°C for 30 min. Transposed DNA was purified using a ChIP DNA Clean & Concentrator Kit (Zymo Research #D5205) and eluted DNA fragments were used to amplify libraries.

value: EC Patient 12

value: Naive CD4 T cells


title: EC Patient 12 ATACseq Total CD4 T cells (1)


title: ART Patient 01 RNAseq Total CD4 T cells


title: EC Patient 12 ATACseq Effector memory CD4 T cells (1)


title: EC Patient 12 ATACseq Central memory CD4 T cells (1)


title: ART Patient 02 RNAseq Total CD4 T cells


title: DLD-1 cells transfected with AID-RanBP2 and treated with Auxin for 4hr Replicate 2

description: Replicate 2

value: cell line

value: Auxin


title: ART Patient 02 RNAseq Effector memory CD4 T cells


title: DLD-1 cells transfected with RanGAP1-WT-FLAG Replicate 1

description: Replicate 1


title: DLD-1 cells transfected with AID-RanBP2 and treated with Auxin for 10hr Replicate 3

description: Replicate 3


title: DLD-1_AID-NeonGreen-TPR_LeptomycinB_2hr_replicate2

description: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Leptomycin B for 2hr replicate2


title: ART Patient 01 RNAseq Naive CD4 T cells

value: ART Patient 01


title: DLD-1 cells transfected with AID-RanBP2 and treated with Auxin for 10hr Replicate 2

description: Replicate 2


title: DLD-1 cells transfected with AID-RanBP2 and treated with Auxin for 10hr Replicate 1

description: Replicate 1


title: EC Patient 11 ATACseq Effector memory CD4 T cells (1)

value: EC Patient 11


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 Replicate 3

description: Replicate 3


title: DLD-1 cells transfected with RanGAP1-KR-FLAG Replicate 1

description: Replicate 1


title: ART Patient 01 RNAseq Central memory CD4 T cells


title: DLD-1 cells transfected with AID-RanBP2 and treated with Auxin for 4hr Replicate 3

description: Replicate 3


title: DLD-1 cells transfected with AID-RanBP2 and treated with Auxin for 4hr Replicate 1

description: Replicate 1


title: EC Patient 10 ATACseq Total CD4 T cells (1)

value: EC Patient 10

value: Total CD4 T cells


title: EC Patient 11 ATACseq TEMRA CD4 T cells (1)

value: TEMRA CD4 T cells


title: DLD-1 cells transfected with AID-RanBP2 Replicate 3

description: Replicate 3


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 Replicate 1

description: Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 and treated with Auxin for 8hr Replicate 3

description: Replicate 3


title: EC Patient 12 ATACseq TEMRA CD4 T cells (1)


title: EC Patient 11 ATACseq Naive CD4 T cells (1)


title: EC Patient 11 ATACseq Total CD4 T cells (1)


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 Replicate 2

description: Replicate 2


title: EC Patient 10 ATACseq TEMRA CD4 T cells (1)


title: EC Patient 11 ATACseq Central memory CD4 T cells (1)

value: Central memory CD4 T cells


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 and treated with Auxin for 2hr Replicate 3

description: Replicate 3


title: EC Patient 10 ATACseq Effector memory CD4 T cells (1)

value: Effector memory CD4 T cells


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 and treated with Auxin for 2hr Replicate 2

description: Replicate 2


title: EC Patient 09 ATACseq TEMRA CD4 T cells (1)

value: EC Patient 09


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 and treated with Auxin for 8hr Replicate 2

description: Replicate 2


title: EC Patient 09 ATACseq Naive CD4 T cells (1)


title: EC Patient 10 ATACseq Central memory CD4 T cells (1)


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 Replicate 2

description: Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 and treated with Auxin for 8hr Replicate 1

description: Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 Replicate 3

description: Replicate 3


title: EC Patient 09 ATACseq Central memory CD4 T cells (1)


title: EC Patient 09 ATACseq Total CD4 T cells (1)


title: DLD-1 cells transfected with AID-NeonGreen-NUP88 and treated with Auxin for 2hr Replicate 1

description: Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 Replicate 1

description: Replicate 1


title: EC Patient 08 ATACseq Total CD4 T cells (1)

value: EC Patient 08


title: EC Patient 10 ATACseq Naive CD4 T cells (1)

value: peripheral blood


title: EC Patient 09 ATACseq Effector memory CD4 T cells (1)


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 and treated with Auxin for 8hr Replicate 1

description: Replicate 1


title: EC Patient 08 ATACseq Naive CD4 T cells (2)


title: EC Patient 08 ATACseq TEMRA CD4 T cells (1)


title: EC Patient 08 ATACseq Effector memory CD4 T cells (2)


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 and treated with Auxin for 8hr Replicate 2

description: Replicate 2


title: EC Patient 08 ATACseq Naive CD4 T cells (1)


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 and treated with Auxin for 2hr Replicate 2

description: Replicate 2


title: EC Patient 08 ATACseq Effector memory CD4 T cells (1)


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 and treated with Auxin for 2hr Replicate 1

description: Replicate 1


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 3  [RNA-Seq]

city: BAR HARBOR

first: Niran

last: Hadad

state: Maine

address: 5 Bloomfield Rd, Unit A

institute: The Jackson Laboratory

data_processing:
Files were aligned to hg19 and peaks were called using MACS2
Reads were trimmed using using trimmomatic and were aligned using to the hg19 genome using bowtie
Peaks were called using MACS standard parameters
Genome_build: hg19
Supplementary_files_format_and_content: Peak file output from MACS2 with samples collapsed across groups
Supplementary_files_format_and_content: DESeq2 normalized gene counts

source_name: U2OS Cells

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: One replicate was ABX treated for 24 hours.

value: Human Bone Osteosarcoma Epithelial Cells

value: U2OS Cells

tag: agent

value: Vehicle (EtOH)

tag: antibody

value: Flag-tagged ER alpha


title: EC Patient 08 ATACseq Central memory CD4 T cells (2)


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 2  [RNA-Seq]


title: EC Patient 07 ATACseq Total CD4 T cells (2)

value: EC Patient 07


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 1   [RNA-Seq]


title: TE5_siNC2 RNA-Seq

city: Los Angeles

first: Qian

last: Yang

state: CA

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
ChIP-Seq pair-end 150bp reads were aligned to the hg19 reference genome using Bowtie2. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

source_name: TE5_siNC2 RNA-Seq

growth_protocol: KYSE150 and TE5 cells are cultured in RPMI-1640 medium, media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL). The Anti-SREBF1 for ChIP-Seq is ProteinTech (lot: 14088-1-AP). The antibody number of KLF5 is sc-398409X from Santa Cruz company.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
Standard Illumina library preparation protocol

treatment_protocol: KYSE150 and TE5 cells knock-down SREBF1 with siRNA and negative control were generated by RNA deepsequencing, in triplicate, using Illumina GAIIx.

value: Esophageal Squamous cell carcinomas cell


title: TE5_KLF5 ChIP-Seq

source_name: TE5_KLF5 ChIP-Seq


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 and treated with Auxin for 8hr Replicate 3

description: Replicate 3

value: cell line

value: Auxin


title: U2OS Cells - ER alpa construct - 10nM 17beta E2 - rep 3  [RNA-Seq]

value: 10nM 17beta E2


title: TE5_siNC1 RNA-Seq

source_name: TE5_siNC1 RNA-Seq


title: TE5_siSREBF1_1 RNA-Seq

source_name: TE5_siSREBF1_1 RNA-Seq


title: TE5_siSREBF1_2 RNA-Seq

source_name: TE5_siSREBF1_2 RNA-Seq


title: EC Patient 07 ATACseq Total CD4 T cells (1)


title: TE5_input ChIP-Seq

source_name: TE5_input ChIP-Seq


title: U2OS Cells - ER alpa construct - 10nM 17beta E2 - rep 1  [RNA-Seq]


title: DLD-1 cells transfected with AID-NeonGreen-NUP214 and treated with Auxin for 2hr Replicate 3

description: Replicate 3


title: U2OS Cells - ER alpa construct - 10nM 17beta E2 - rep 2  [RNA-Seq]


title: EC Patient 07 ATACseq Naive CD4 T cells (2)

value: Naive CD4 T cells


title: KYSE150_input ChIP-Seq

source_name: KYSE150_input ChIP-Seq


title: EC Patient 07 ATACseq Naive CD4 T cells (1)


title: EC Patient 07 ATACseq TEMRA CD4 T cells (1)


title: KYSE150_SREBF1 ChIP-Seq

source_name: KYSE150_SREBF1 ChIP-Seq


title: U2OS Cells - ER alpa construct - 100nM 17alpha E2 - rep 3 [RNA-Seq]

value: 100nM 17alpha E2


title: EC Patient 07 ATACseq Effector memory CD4 T cells (2)


title: TE5_SREBF1 ChIP-Seq

source_name: TE5_SREBF1 ChIP-Seq


title: EC Patient 08 ATACseq Central memory CD4 T cells (1)


title: EC Patient 07 ATACseq Effector memory CD4 T cells (1)


title: U2OS Cells - ER alpa construct - 100nM 17alpha E2 - rep 2 [RNA-Seq]


title: U2OS Cells - ER alpa construct - 100nM 17alpha E2 - rep 1  [RNA-Seq]


title: EC Patient 07 ATACseq Central memory CD4 T cells (2)


title: U2OS Cells - ER alpa construct - 10nM 17alpha E2 - rep 3 [RNA-Seq]

value: 10nM 17alpha E2


title: EC Patient 07 ATACseq Central memory CD4 T cells (1)

value: Central memory CD4 T cells


title: U2OS Cells - ER alpa construct - 10nM 17alpha E2 - rep 2 [RNA-Seq]


title: EC Patient 06 ATACseq Total CD4 T cells (1)

source_name: Total CD4 T cells

value: EC Patient 06

value: Total CD4 T cells


title: U2OS Cells - ER alpa construct - 10nM 17alpha E2 - rep 1  [RNA-Seq]


title: EC Patient 06 ATACseq Naive CD4 T cells (1)


title: EC Patient 06 ATACseq TEMRA CD4 T cells (1)

value: TEMRA CD4 T cells


title: Female FxrShoKO LiverCancer 3

city: Houston

first: Yun Seong

last: Jeong

state: TX

address: 6565 MD Anderson Blvd.

institute: MD Anderson Cancer Center

description:
9394274006_C.AVG_Signal
Female.FxrShpKO.LiverCancer_3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina mouse WG-6 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: Female DKO Tumor

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000).

growth_protocol: 1-year-old mice were used.

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: strain

value: Fxr Sho DKO

value: Liver

tag: Sex

value: Female

value: 1 year


title: Female FxrShoKO LiverCancer 6

description:
9394274006_F.AVG_Signal
Female.FxrShpKO.LiverCancer_6
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 4 [RNA-Seq]

value: Human Bone Osteosarcoma Epithelial Cells

value: U2OS Cells

value: Vehicle (EtOH)

value: 10percent input


title: EC Patient 06 ATACseq Effector memory CD4 T cells (1)

source_name: Effector memory CD4 T cells

value: peripheral blood

value: Effector memory CD4 T cells


title: U2OS Cells - ER beta construct - Vehicle (EtOH) - rep 5 [RNA-Seq]


title: Female WT NormLiver 6

description:
9370689057_F.AVG_Signal
Female.WT.NormLiver_6
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

source_name: Female WT liver

value: WT


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 3 [RNA-Seq]

value: Flag-tagged ER alpha


title: Female FxrShoKO LiverCancer 5

description:
9394274006_E.AVG_Signal
Female.FxrShpKO.LiverCancer_5
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Female FxrShoKO LiverCancer 2

description:
9394274006_B.AVG_Signal
Female.FxrShpKO.LiverCancer_2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: EC Patient 06 ATACseq Central memory CD4 T cells (1)

source_name: Central memory CD4 T cells


title: Female FxrShoKO LiverCancer 1

description:
9394274006_A.AVG_Signal
Female.FxrShpKO.LiverCancer_1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Female FxrShoKO LiverCancer 4

description:
9394274006_D.AVG_Signal
Female.FxrShpKO.LiverCancer_4
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 2 [RNA-Seq]


title: Female WT NormLiver 2

description:
9370689057_B.AVG_Signal
Female.WT.NormLiver_2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Female WT NormLiver 5

description:
9370689057_E.AVG_Signal
Female.WT.NormLiver_5
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: EC Patient 05 ATACseq Total CD4 T cells (1)

value: EC Patient 05


title: Male FxrShoKO LiverCancer 3

description:
9237299033_C.AVG_Signal
Male.FxrShpKO.LiverCancer_3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

source_name: Male DKO Tumor

value: Male


title: Female WT NormLiver 1

description:
9370689057_A.AVG_Signal
Female.WT.NormLiver_1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Male FxrShoKO LiverCancer 5

description:
9237299033_E.AVG_Signal
Male.FxrShpKO.LiverCancer_5
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Male FxrShoKO LiverCancer 4

description:
9237299033_D.AVG_Signal
Male.FxrShpKO.LiverCancer_4
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Male FxrShoKO LiverCancer 2

description:
9237299033_B.AVG_Signal
Male.FxrShpKO.LiverCancer_2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Female WT NormLiver 4

description:
9370689057_D.AVG_Signal
Female.WT.NormLiver_4
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: U2OS Cells - ER alpa construct - Vehicle (EtOH) - rep 1  [RNA-Seq]


title: Male WT NormLiver 6

description:
9237299025_F.AVG_Signal
Male.WT.NormLiver_6
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

source_name: Male WT liver


title: Female WT NormLiver 3

description:
9370689057_C.AVG_Signal
Female.WT.NormLiver_3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Male FxrShoKO LiverCancer 6

description:
9237299033_F.AVG_Signal
Male.FxrShpKO.LiverCancer_6
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: EC Patient 05 ATACseq TEMRA CD4 T cells (1)

source_name: TEMRA CD4 T cells


title: Male WT NormLiver 5

description:
9237299025_E.AVG_Signal
Male.WT.NormLiver_5
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: U2OS Cells - ER alpa construct - 10nM 17beta E2 - rep 3 [ChIP-Seq]

source_name: U2OS Cells

value: 10nM 17beta E2


title: EC Patient 05 ATACseq Naive CD4 T cells (1)

source_name: Naive CD4 T cells

value: Naive CD4 T cells


title: Multiple libraries 1

city: Stanford

first: Ricardo

last: Fernandes

state: California

address: 279 Campus Drive

department: Molecular and Cellular Physiology

institute: Stanford University

description: Naïve, Fat TCR, Effector TCR

data_processing:
Alignment of forward and reverse reads using pandaseq.
Raw sequences were converted to clustal.
Sequence files were parsed for sequences containing the plasmid backbone sequences: GTTTTG and GGCGGTGG.
DNA sequences were translated to amino acid format.
Stop sequences were removed.
The number of reads per peptide sequence was determined as described in Birnbaum M., et al, Cell, 2014 and Gee, M., et al., Cell, 2018.
Genome_build: NA
Supplementary_files_format_and_content: *.csv: Number of counts for each unique peptide identified for each round of selection and Naive, pre-TCR selected library.

organism: synthetic construct

source_name: Synthetic DNA/peptide library

growth_protocol: Yeast were grown in SDCAA and pMHC was induced in SGCAA.

extract_protocol:
Zymoprep was used to extract the plasmid containing the gene for the peptide-MHC.
Peptide library was encoded in an appropriate oligo using degenerate oligos (e.g. NNK) where appropriate and as described in the manuscript.
The naive library and round 1, 2 and 3 were incubated with magnetic-streptavidin beads coated with TCR of interest at 400 nM. After incubation for 3 hours at 4C, the fraction of TCR bound beads was isolated using LS magnetic columns (Miltenyi). For round 4 of the Pmhc selection a TCR-streptavidin tetramer was used iin place of the streptavidin-beads.

treatment_protocol: Yeast were selected after binding to TCR of interest. Unbound fraction was discarded. TCR bound yeast were isolated and expanded.

value: Isolated from Yeast


title: U2OS Cells - ER alpa construct - 10nM 17beta E2 - rep 2 [ChIP-Seq]


title: EC Patient 05 ATACseq Central memory CD4 T cells (1)

value: Central memory CD4 T cells


title: EC Patient 05 ATACseq Effector memory CD4 T cells (1)


title: Multiple libraries 2

description: 2W TCR


title: U2OS Cells - ER alpa construct - 10nM 17beta E2 - rep 1  [ChIP-Seq]


title: U2OS Cells - ER alpa construct - 100nM 17alpha E2 - rep 3 [ChIP-Seq]

value: 100nM 17alpha E2


title: EC Patient 04 ATACseq Total CD4 T cells (1)

value: EC Patient 04

value: Total CD4 T cells


title: dis3-1

city: Oxford

first: Adrien

last: Birot

address: South Parks Rd

department: Departement of Biochemistry

institute: University of Oxford

data_processing:
Sequenced reads and quality trimming was performed using Trimmomatic (Galaxy Version 0.32.3, RRID:SCR_011848)
Aligned to the concatenated S. pombe (ASM294v2.19) using Bowtie 2
Reads mapped only once were obtained by SAMTools
Total read count normalisation using DEseq2 was used
Genome_build: S. pombe genome (ASM294v2.19)
Supplementary_files_format_and_content: bedgraph

organism: Schizosaccharomyces pombe

source_name: dis3-54 mutant (YP67)

growth_protocol: cultures on EMMG+uracil (10mg/ml) to mid-log phase, at 30°C

extract_protocol:
Sample is subjected to proteinase K tratement during 1h, then standard hot phenol method was used to recover ultra-pure poly(A)+ RNA
Library preparation was performed with NEBNext Ultra Direational RNA Library Prep Kit for Illumina (NEB #E7420) and the NEBNext Multiplex Oligos for Illumina (Set 1, NEB #7335)  by using 100ng of RNA as starting material.
Paired-end sequencing of the pooled libraries was carried out on an Illumina NextSeq 500 on four lanes (L1-L4)

treatment_protocol: After cross-linking procedure described in Kilchert C et al. 2020 (PMID: 31883228), frozen cell pellets were lysed by grinding under liquid N2 for 20-25 min and resuspended in oligo d(T) lysis buffer (20 mM Tris-HCl pH 7.5, 500 mM LiCl, 0.5% LiDS, 1 mM EDTA; 5 mM DTT, protease inhibitor cocktail IV (fungal) 1:10,000; add DTT and protease inhibitor freshly). Then lysate was centrifuged twice for extract clarification and the supernatant was subject to pull-dow using magnetic oligo-dT beads during 1h at 4°C with rotation. Then immobilzed magnetic oligo-dT beads were washed (20 mM Tris-HCl pH 7.5, 500 mM LiCl, 0.1% LiDS, 1 mM EDTA, 5 mM DTT and 20 mM Tris-HCl pH 7.5, 500 mM LiCl, 1 mM EDTA and  20 mM Tris-HCl pH 7.5, 200 mM LiCl, 1 mM EDTA) and eluated in 20 mM Tris-HCl pH 7.5, 1 mM EDTA.

tag: genotype/variation

value: dis3-54 mutant


title: dis3-3


title: dis3-2


title: U2OS Cells - ER alpa construct - 100nM 17alpha E2 - rep 2 [ChIP-Seq]

value: Human Bone Osteosarcoma Epithelial Cells

value: U2OS Cells


title: rrp6-3

source_name: rrp6delta mutant (YP411)

value: rrp6delta mutant


title: U2OS Cells - ER alpa construct - 100nM 17alpha E2 - rep 1  [ChIP-Seq]


title: rrp6-1


title: Male FxrShoKO LiverCancer 1

description:
9237299033_A.AVG_Signal
Male.FxrShpKO.LiverCancer_1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

value: Fxr Sho DKO

value: Liver

tag: age

value: 1 year


title: Male WT NormLiver 2

description:
9237299025_B.AVG_Signal
Male.WT.NormLiver_2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

value: WT


title: Male WT NormLiver 3

description:
9237299025_C.AVG_Signal
Male.WT.NormLiver_3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Male WT NormLiver 1

description:
9237299025_A.AVG_Signal
Male.WT.NormLiver_1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: mtl1-3

source_name: mtl1-1 mutant (YP729)

value: mtl1-1 mutant


title: EC Patient 04 ATACseq Naive CD4 T cells (1)

value: peripheral blood


title: mtl1-2


title: EC Patient 04 ATACseq Effector memory CD4 T cells (1)

value: Effector memory CD4 T cells


title: U2OS Cells - ER alpa construct - 10nM 17alpha E2 - rep 3 [ChIP-Seq]

tag: cell line

value: 10nM 17alpha E2

value: Flag-tagged ER alpha


title: PGL primary tumor

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridized according to a established protocol by Agilent Technologies (Santa Clara, CA, USA)

scan_protocol: Images were scanned using Agilent scanner, G2565BA

data_processing: The data were normalized using the method  normexp in order to eliminate the background (Herrero et al.,Nucleic Acids Research, 2003) and limma library by Bioconductor ( Performing loess for intra-array correction and quantiles for inter-array correction)[Smyth et al., Bioinformatics, 2005].

source_name: PGL primary tumor

label_protocol: 0.5 ug of tumoral amplified RNA was labeled with Cy5 and the same amount of the reference (Universal reference RNA from Stratagene) was labeled with Cy3

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
Amplified RNA - MMLV-RT

tag: disease state

value: paraganglioma

value: Primary tumor

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: collection of RNA pooled from ten cell lines  (Adenocarcinoma, mammary gland Hepatoblastoma, liver Adenocarcinoma, cervix Embryonal carcinoma, testis Glioblastoma, brain Melanoma Liposarcoma Histiocytic lymphoma; macrophase; histocyte Lymphoblastic leukemiaPlasmacytoma; myeloma; B lymphocyte)


title: mtl1-1


title: U2OS Cells - ER alpa construct - 10nM 17alpha E2 - rep 1  [ChIP-Seq]


title: WT-2

source_name: wild-type (YP144)

value: wild-type


title: WT-3


title: EC Patient 03 ATACseq Total CD4 T cells (1)

source_name: Total CD4 T cells

tag: patient

value: EC Patient 03

value: Total CD4 T cells


title: EC Patient 04 ATACseq Central memory CD4 T cells (1)

value: EC Patient 04

tag: replicate

value: Central memory CD4 T cells


title: Male WT NormLiver 4

description:
9237299025_D.AVG_Signal
Male.WT.NormLiver_4
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

value: Male


title: EC Patient 04 ATACseq TEMRA CD4 T cells (1)

value: TEMRA CD4 T cells


title: rrp6-2

value: rrp6delta mutant


title: WT-1


title: EC Patient 03 ATACseq TEMRA CD4 T cells (1)


title: T_cell_ChIP_T_input_rep1

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl, Memphis, TN

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: ChIP-seq

data_processing:
BWA mem mapping to hg38
generate MACS2 signal tracks: macs2 callpeak -t -c  -g hs --keep-dup all -B
Generate normalized signals (fold enrichment): macs2 bdgcmp -t treat_pileup.bdg -c control_lambda.bdg -m FE -o FE.bdg
Genome_build: hg38
Supplementary_files_format_and_content: bw

growth_protocol: Human primary CD4+/CD8+ T-cells were cultured in X-Vivo 15 media (Lonza) supplemented with 5% human heat-inactivated serum (Fisher), 10 ng/ml IL-7 (Miltenyi), and 10 ng/ml IL-15 (Miltenyi). T-cells were stimulated with MACS GMP T-cell TransAct polymeric nanomatrix (Miltenyi) for 3 days according to the manufacturer’s instructions prior to transfection.

extract_protocol: Sequencing libraries were generated using NEBNext Ultra II DNA library Prep kit (NEB, E7645). Custom TruSeq adaptors were used. Libraries were sequenced with 50 bp single-end reads using Illumina HiSeq 4000.

value: Human primary CD4/CD8 T cells


title: RM3-3d

city: Cheongju-si

first: Hanseul

last: Oh

state: Chungcheongbuk-do

address: 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu,

country: South Korea

institute: Korea Research Institute of Bioscience & Biotechnology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Macaca mulatta (NCBI) whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: Macaca mulatta (NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: PBMC

tag: gender

tag: infection status

value: 3 days post infection with SARS-CoV-2


title: RM2-3d

tag: tissue

value: Female


title: EC Patient 03 ATACseq Naive CD4 T cells (1)

value: peripheral blood

value: Naive CD4 T cells


title: RM4-2w

value: Before SARS-CoV-2 infection


title: T_cell_ChIP_input_rep2

description: ChIP-seq


title: U2OS Cells - ER alpa construct - 10nM 17alpha E2 - rep 2 [ChIP-Seq]

value: Human Bone Osteosarcoma Epithelial Cells

value: U2OS Cells

value: 10nM 17alpha E2

value: Flag-tagged ER alpha


title: RM3-2w


title: EC Patient 03 ATACseq Effector memory CD4 T cells (1)

source_name: Effector memory CD4 T cells

value: EC Patient 03

value: Effector memory CD4 T cells


title: T_cell_ChIP_T_H3K36me3_rep2

description: ChIP-seq

value: H3K36me3 (ab9050, Abcam)


title: T_cell_ChIP_H3K36me3_rep1

description: ChIP-seq


title: RM1-3d


title: EC Patient 03 ATACseq Central memory CD4 T cells (1)

value: Central memory CD4 T cells


title: RM1-2w


title: T_cell_ChIP_H3K27ac_rep2

description: ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: T_cell_ChIP_H3K27me3_rep2

description: ChIP-seq

value: H3K27me3 (ab6002, Abcam)


title: EC Patient 02 ATACseq TEMRA CD4 T cells (1)

value: EC Patient 02

value: TEMRA CD4 T cells


title: T_cell_ChIP_H3K27ac_rep1

description: ChIP-seq

value: Human primary CD4/CD8 T cells


title: EC Patient 02 ATACseq Effector memory CD4 T cells (1)


title: T_cell_ChIP_H3K9ac_rep2

description: ChIP-seq

value: H3K9ac (ab10812, Abcam)


title: RM2-2w

value: PBMC

value: Female


title: RNA-seq_UTX_KO1_rep3

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

description: RNA-seq_ReadCount.txt,UTX_KO_WT_Diff.txt

data_processing:
High-quality reads of RNA-seq were quantified using Salmon (v.1.1.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).
Genome_build: GRCh38

source_name: Human neurons from hESCs

growth_protocol: The human H9 (WA09) ESC line was obtained from Dr. Baoyang Hu at the Institute of Zoology, Chinese Academy of Sciences. H9 cells were cultured on Matrigel (BD, New Jersey, USA) using TeSR™-E8™ (STEMCELL Technologies, Vancouver, BC, Canada) and passaged with EDTA (100 μM). Neural differentiation of the H9 cells was initiated by the formation of embryoid bodies (EBs) as described previously with minor modifications (Jiang et al., 2013). Briefly, hESC colonies were dissociated with Accutase (BD, New Jersey, USA) and resuspended as single cells in E8 medium with 10μM Rock inhibitor （Y27632, Selleck, Shanghai, China）. To produce EBs from hESCs, hESCs medium was replaced with N2 medium（DMEMF/12, 1xN2, 1xNEAA) at day 3 and medium was changed every other day. To obtain NPCs derived from hESCs，the EBs were plated at day 7 on Matrigel-coated plates with 1μg/ml laminin (Life Technologies, Carlsbad, CA, USA) and cultured in N2 medium . NPCs in the form of rosettes were manually picked at day 14 and expanded as neurospheres in N2B27 medium (DMEM/F12, 1xN2, 1xB27, 0.2μM RA and 20ng/ml FGF2) until day 20. For neuronal differentiation, the dissociated NPCs at day 20 were plated onto poly-L-ornithine/laminin (50 μg/ml)-coated coverslips, and cultured in neuronal differentiation medium (DMEM/F12, 1xN2, 1xB27, 10ng/ml BDNF, 10ng/ml GDNF, 1mM dibutryrl-cyclic AMP and 200 nM ascorbic acid).

extract_protocol:
We isolated hESCs-derived neurons at day 40 in culture. Total RNAs were extracted using TRIzol reagent.
RNA-seq libraries were from the d40 neurons. Total RNA sample QC was measured by Illumina NovaSeq 6000.

treatment_protocol: We isolated hESCs-derived neurons at day 40 in culture. Total RNAs were extracted using TRIzol reagent, and sequenced on novaSeq 6000 system. ChIP was performed as described previously (Liu et al., 2010). ChIP-seq libraries were sequenced generating 50-bp single reads.

tag: passages

value: UTX-/-


title: RNA-seq_UTX_KO1_rep1


title: RNA-seq_UTX_KO1_rep2


title: EC Patient 02 ATACseq Naive CD4 T cells (1)

value: peripheral blood

tag: cell type

value: Naive CD4 T cells


title: EC Patient 02 ATACseq Central memory CD4 T cells (1)

source_name: Central memory CD4 T cells


title: EC Patient 01 ATACseq Total CD4 T cells (1)

value: EC Patient 01

value: Total CD4 T cells


title: RNA-seq_UTX_KO2_rep2

tag: genotype


title: RNA-seq_WT-rep3

value: Wild type


title: RNA-seq_WT-rep2


title: EC Patient 01 ATACseq TEMRA CD4 T cells (1)


title: EC Patient 02 ATACseq Total CD4 T cells (1)


title: RNA-seq_WT-rep1


title: siNBAS rep5

description: siNBAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were pseudoaligned using kallisto v0.43.1 to kallisto index created by combining “all basic gene annotation” and “long non-coding RNA gene annotation” fasta files, downloaded from Gencode (www.gencodegenes.org/releases/current.html), Release 27 (GRCh38.p10). Kallisto was run with 100 bootstraps.
Differential gene expression was analysed using DESeq2 v1.14.1
Genome_build: hg38
Supplementary_files_format_and_content: kallisto output:  tab-delimited text files for each sample with RPKM values for each gene.

source_name: HeLa cells

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Cat#NEB #E7103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: samples were double depleted with siRNA pool against UPF1 or NBAS, or si-scr control

value: HeLa

tag: knockdown

value: siNBAS


title: T_cell_ChIP_H3K9me3_rep2

description: ChIP-seq

tag: antibody

value: H3K9me3 (ab8898, Abcam)


title: T_cell_ChIP_H3K27me3_rep1

description: ChIP-seq


title: RNA-seq_UTX_KO2_rep1


title: EC Patient 01 ATACseq Naive CD4 T cells (1)


title: T_cell_ChIP_H3K4me3_rep2

description: ChIP-seq

value: H3K4me3 (9751, Cell signaling)


title: siNBAS rep3

description: siNBAS


title: T_cell_ChIP_H3K9ac_rep1

description: ChIP-seq


title: siNBAS rep2

description: siNBAS


title: EC Patient 01 ATACseq Effector memory CD4 T cells (1)

value: Effector memory CD4 T cells


title: siNBAS rep1

description: siNBAS


title: siUPF1 rep5


title: T_cell_ChIP_H3K4me3_rep1

description: ChIP-seq


title: siUPF1 rep4


title: siUPF1 rep3


title: EC Patient 01 ATACseq Central memory CD4 T cells (1)

value: Central memory CD4 T cells


title: ART Patient 03 ATACseq Total CD4 T cells (2)

value: ART Patient 03


title: T_cell_ChIP_H3K4me1_rep2

description: ChIP-seq

value: Human primary CD4/CD8 T cells

value: H3K4me1 (ab8895, Abcam)


title: siNBAS rep4

description: siNBAS


title: siScr rep4

description: siScr control

value: siScr control


title: T_cell_ChIP_H3K4me1_rep1

description: ChIP-seq


title: ART Patient 03 ATACseq Total CD4 T cells (1)


title: siScr rep5

description: siScr control


title: ΔbigR mTn7(bigRC34A/C100A) rep3

city: Bloomington

first: David

middle: Peter

last: Giedroc

state: IN

address: 212 S. Hawthorne Drive

department: Chemistry

institute: Indiana University

description: geneCountsPrimary.xlsx

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version 2.20.0 pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
Reads were mapped to the transcriptome using Bowtie2 (version 2.3.4.3)
Reads mapped to transcripts were counted using Samtools (version version 1.9 ) and featureCounts (version 1.6.4)
R (version 3.6.0) and DESeq2 (version 1.24.0) were used to perform differential expresison analysis.
Genome_build: Acinetobacter_baumannii_atcc_17978.ASM1542v1.dna.chromosome.Chromosome.fa (ENSEMBL Release 43)
Supplementary_files_format_and_content: tab-delimited text file of raw count values for each Sample ...

organism: Acinetobacter baumannii

source_name: Exponentially grown cells

growth_protocol: Overnight cultures of A. baumannii 17978 were grown in LB medium overnight and used to inoculate 3mL LB medium at a 1:50 dilution and grown aerobically at 37°C with shaking at 200 rpm for 1 h. These cultures were then diluted 1:100 in fresh LB medium and grown under identical conditions until OD600=0.2.

extract_protocol:
Following growth and treatment, 10mL aliquots of cells were pelleted and resuspended in 1mL TriReagent (Molecular Research Center), then lysed with 0.1mm silica beads in a bead beater (MP Bio). RNA was extracted by adding 200 uL chloroform, mixing, and centrifuging. The aqueous layer was extracted and added to one volume of 70% ethanol. RNA purification was completeted using the RNeasy minikit (Qiagen).
First, the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. From each sample, 1ug of total RNA was used for ribosome RNA depletion with the Invitrogen™ RiboMinus™ Transcriptome Isolation Kit, bacteria.  After rRNA depletion, the libraries were prepared following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads.

treatment_protocol: Sample 2 only

tag: strain

tag: mutation

value: ΔbigR mTn7(bigRC34A/C100A)


title: ART Patient 03 ATACseq TEMRA CD4 T cells (2)

source_name: TEMRA CD4 T cells

value: TEMRA CD4 T cells


title: siScr rep3

description: siScr control


title: ART Patient 03 ATACseq TEMRA CD4 T cells (1)

value: peripheral blood


title: ART Patient 03 ATACseq Naive CD4 T cells (2)

value: Naive CD4 T cells


title: ΔbigR mTn7(bigRC34A/C100A) rep1

description: geneCountsPrimary.xlsx


title: siScr rep1

description: siScr control


city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
D2_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) from the 3D connective airways tissue in vitro, rep2

data_processing:
Sequence reads were trimmed using Trim Galore software (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality end bases and then aligned on hg38 reference sequence using STAR.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_unique_counts.txt.gz: Tab-delimited text files include raw counts for each Sample.

source_name: Primary cells

growth_protocol: Human Lung Fibroblasts (Normal and Cystic Fibrosis) from Lonza were grown in Minimum Essential Medium supplemented with 20% FBS, 2% Non-Essential Amino Acids, 1% Pen/Sprep.

extract_protocol:
Tissues were collected in Trizol and mechanically homogenized. RNA was extracted by phenol-chloroform method and further purified using Roche column (from the kit 12033647001). RNA was quantified and mixed at 10ng/µl.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp.

treatment_protocol: Both Normal and Cystic Fibrosis fibroblasts were treated with Ascorbic Acid (0.5mM) in order to guarantee collagen synthesis.

value: Cystic Fibrosis Lung Fibroblasts

tag: culture type

tag: donor age

value: 45 years

value: Female


title: ΔbigR mTn7(bigRC34A/C100A) rep2

description: geneCountsPrimary.xlsx


description:
D3_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) from the 3D connective airways tissue in vitro, rep3


title: siScr rep2

description: siScr control

tag: cell line

value: HeLa


title: ΔbigR rep3

description: geneCountsPrimary.xlsx

value: ΔbigR


title: ART Patient 03 ATACseq Naive CD4 T cells (1)

last: Gao

source_name: Naive CD4 T cells


description:
N3_unique
Transcriptome profile of Normal Human Lung Fibroblasts from the 3D connective airways tissue in vitro, rep3

value: Normal Lung Fibroblasts

value: 47 years

value: Male


description:
N2_unique
Transcriptome profile of Normal Human Lung Fibroblasts from the 3D connective airways tissue in vitro, rep2


title: ΔbigR rep1

description: geneCountsPrimary.xlsx


description:
N1_unique
Transcriptome profile of Normal Human Lung Fibroblasts from the 3D connective airways tissue in vitro, rep1


title: Disease Human Lung Fibroblasts (Cystic Fibrosis) from 2D culture, rep4

description:
D4_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) in 2D culture, rep4

extract_protocol:
Cells were collected in Trizol and RNA was extracted by phenol-chloroform method and further purified using Roche column (from the kit 12033647001). RNA was quantified and mixed at 10ng/µl.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp.

treatment_protocol: Cells were not treated with specific substances.


title: ART Patient 03 ATACseq Effector memory CD4 T cells (1)

value: Effector memory CD4 T cells


description:
D1_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) from the 3D connective airways tissue in vitro, rep1


title: Disease Human Lung Fibroblasts (Cystic Fibrosis) from 2D culture, rep3

description:
D3_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) in 2D culture, rep3


title: T_cell_ChIP_H3K9me3_rep1

description: ChIP-seq

value: H3K9me3 (ab8898, Abcam)


title: WT sulfide treated rep3

description: geneCountsPrimary.xlsx

treatment_protocol:
Na2S was added to the cultures at a ﬁnal concentration of 0.2 mM when the OD600 reached 0.2
Sample 2 only

tag: treatment

value: sodium sulfide


title: Tumor carrying a DLST mutation 3

type: genomic

description:
SAMPLE 6
genomic DNA from a tumor carrying a DLST mutation

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio software v2011

label: Cy5 and Cy3

source_name: Primary tumor 6

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: pheochromocytoma/paraganglioma

value: female

value: Primary tumor

value: tumor carrying a DLST mutation


title: Disease Human Lung Fibroblasts (Cystic Fibrosis) from 2D culture, rep2

description:
D2_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) in 2D culture, rep2


title: Normal Human Lung Fibroblasts from 2D culture, rep4

description:
N4_unique
Transcriptome profile of Normal Human Lung Fibroblasts in 2D culture, rep4


title: WT sulfide treated rep2

description: geneCountsPrimary.xlsx


title: Normal Human Lung Fibroblasts from 2D culture, rep1

description:
N1_unique
Transcriptome profile of Normal Human Lung Fibroblasts in 2D culture, rep1


title: ART Patient 03 ATACseq Central memory CD4 T cells (1)

tag: patient

value: ART Patient 03

value: peripheral blood

value: Central memory CD4 T cells


title: Normal Human Lung Fibroblasts from 2D culture, rep2

description:
N2_unique
Transcriptome profile of Normal Human Lung Fibroblasts in 2D culture, rep2


title: Rested-0hr-donor-207_S6

first: Ying-Lin Stefanie

last: Tan

address: 1 Portland St

institute: Pfizer

data_processing:
UMI were generated using the QIASeq Tageted RNA Analysis Software
Reads were mapped to GRCh38 reference genome and alignment done using the STAR method.
Differential expression was calculated using the DESeq2 app in Illumina's Basespace Labs, according to the method described in Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. http://doi.org/10.1186/s13059-014-0550-8.
Genome_build: hg38

source_name: CD4+ T cells

growth_protocol: Primary human CD4+ T cells were isolated from frozen hPBMCs

extract_protocol:
RNA was extracted from frozen cell pellets using the Qiagen RNAeasy mini isolation kit, and 200ng RNA used in the construction of libraries.
Sequencing libraries were prepared using a Qiagen Targeted custom metabolic panel designed for the QiaSeq Target RNA kit, followed by Sw Illumina TruSeq Stranded mRNA Library Prep (cat.20020594) according to standard protocols.

treatment_protocol: Cells were activated for 24 hr in the presence of indicated treatment regimens, then washed and cell pellets flash frozen.

value: CD4+ T cells

tag: activation state

value: Rested

value: Water


title: Normal Human Lung Fibroblasts from 2D culture, rep3

description:
N3_unique
Transcriptome profile of Normal Human Lung Fibroblasts in 2D culture, rep3

tag: gender


title: ART Patient 02 ATACseq Total CD4 T cells (1)

value: ART Patient 02

tag: replicate

value: Total CD4 T cells


title: Rested-0hr-donor-44_S3

tag: tissue


title: RM4-3d

value: PBMC

tag: infection status

value: 3 days post infection with SARS-CoV-2


title: Disease Human Lung Fibroblasts (Cystic Fibrosis) from 2D culture, rep1

description:
D1_unique
Transcriptome profile of Disease Human Lung Fibroblasts (Cystic Fibrosis) in 2D culture, rep1

tag: cell type

value: Cystic Fibrosis Lung Fibroblasts

value: 45 years

value: Female


title: Metformin-2DG-Activated-24hr-donor-207_S5

value: Activated

value: Metformin, 2-DG


title: ART Patient 02 ATACseq Total CD4 T cells (2)


title: WT sulfide treated rep1

description: geneCountsPrimary.xlsx

value: sodium sulfide


title: WT untreated rep2

description: geneCountsPrimary.xlsx


title: ART Patient 02 ATACseq TEMRA CD4 T cells (1)

value: TEMRA CD4 T cells


title: WT untreated rep1

description: geneCountsPrimary.xlsx


title: Metformin-2DG-Activated-24hr-donor-44_S2


title: Rrp40-D87A

first: Derrick

middle: Jerone

last: Morton

address: 1510 Clifton Rd NE

department: Biology

institute: Emory

data_processing:
The reads were mapped to the BDGP D. melanogaster (r6.25) genome. Several sequence datasets were downloaded from GenBank and FlyBase for initial assessment of the data including: 1) All Drosophila ribosomal sequences found in Genbank: Drosophila_rRNA.fa; 2) All FlyBase D. melanogaster transcripts from assembly r6.25: dmel_transcripts_r6.25.fa. Adapters were trimmed from raw reads using Trimmomatic (ver. 0.36), and trimmed reads were aligned to the ribosomal sequences using Bowtie2, and only reads which did not map to the ribosome were kept for downstream analysis.
Non-ribosomal reads were then mapped to D. melanogaster r6.25 using Tophat2. The resulting aligned reads were compared using DESeq2

source_name: Head Tissue

extract_protocol:
Adult fly heads were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: fly strain

value: Head tissue

tag: age

value: Day 0

tag: genotype


title: Rrp40-G11A


title: ART Patient 02 ATACseq Naive CD4 T cells (2)

extract_protocol:
DNA was treated with Tn5 and purified using Chip dna clean & concentrator
20,000 sorted cells were centrifuged at 1500 rpm for 10 min at 4°C in a pre-cooled fixed-angle centrifuge. All supernatant was removed and a modified transposase mixture (including 25 µl of 2x TD buffer, 1.5 µl of TDE1, 0.5 µl of 1% digitonin, 16.5 µl of PBS, 6.5 µl of nuclease-free water) was added to the cells and incubated in a heat block at 37°C for 30 min. Transposed DNA was purified using a ChIP DNA Clean & Concentrator Kit (Zymo Research #D5205) and eluted DNA fragments were used to amplify libraries.

value: peripheral blood

value: Naive CD4 T cells


title: Metformin-2DG-Activated-9hr-donor-44_S16

value: CD4+ T cells


title: Tumor carrying a DLST mutation 2

description:
SAMPLE 5
genomic DNA from a tumor carrying a DLST mutation

source_name: Primary tumor 5

value: pheochromocytoma/paraganglioma

value: female

value: Primary tumor

value: tumor carrying a DLST mutation


title: Rrp40-WT


title: CM4-3d

organism: Macaca fascicularis

value: PBMC

value: 3 days post infection with SARS-CoV-2


title: Metformin-2DG-Activated-9hr-donor-207_S18


title: ART Patient 02 ATACseq Effector memory CD4 T cells (2)

value: ART Patient 02

value: Effector memory CD4 T cells


title: Tumor carrying a EPAS1 mutation

description:
SAMPLE 3
genomic DNA from a tumor carrying a EPAS1 mutation

source_name: Primary tumor 3

value: tumor carrying a EPAS1 mutation


title: CM4-2w

value: Female

value: Before SARS-CoV-2 infection


title: ART Patient 02 ATACseq Effector memory CD4 T cells (1)


title: Tumor carrying a MAX mutation 2

description:
SAMPLE 2
genomic DNA from a tumor carrying a MAX mutation

source_name: Primary tumor 2

value: male

value: tumor carrying a MAX mutation


title: Tumor carrying a DLST mutation 1

description:
SAMPLE 4
genomic DNA from a tumor carrying a DLST mutation

source_name: Primary tumor 4


title: CM3-2w


title: CM3-3d


title: Metformin-2DG-Activated-6hr-donor-207_S14

value: Activated

value: Metformin, 2-DG


title: ART Patient 02 ATACseq Naive CD4 T cells (1)

value: peripheral blood

value: Naive CD4 T cells


title: ART Patient 03 ATACseq Central memory CD4 T cells (2)

value: ART Patient 03

value: Central memory CD4 T cells


title: Female, Peritoneal cavity macrophages

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
Illumina Novaseq S1 software used for basecalling
Initial processing was done using Cell Ranger (v2.1.1) mkfastq and count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Peritoneal cavity macrophages

growth_protocol: Cells were obtained by peritoneal lavage with RPMI supplemented with 2mM EDTA and 10mM HEPES according to PMID 29761387

extract_protocol: As per 10x genomics protocol (10K cells were loaded per each sample)

treatment_protocol: Cells were stained for FACS according to PMID 29761387 and target populations sorted to high purity

value: Peritoneal cavity macrophages

tag: gating strategy

value: Live CD45+ CD11b+ SiglecF- CD19- CD3- Ly6G-

tag: Sex

value: female

tag: strain

value: 19 weeks


title: Male, Peritoneal cavity macrophages


title: Metformin-2DG-Activated-6hr-donor-44_S12

value: CD4+ T cells


title: Tumor carrying a MAX mutation 1

description:
SAMPLE 1
genomic DNA from a tumor carrying a MAX mutation

source_name: Primary tumor 1

value: pheochromocytoma/paraganglioma

value: Primary tumor


title: ART Patient 02 ATACseq Central memory CD4 T cells (2)

first: Ce

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
Reads were trimmed for adaptor sequence, then mapped to GRCh38 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using MACS2. For duplicated samples, peaks were merge using Bioconductor.
Genome_build: GRCh38
Supplementary_files_format_and_content: summits in BED

value: ART Patient 02


title: CM2-3d

source_name: PBMC

value: PBMC

value: Male

value: 3 days post infection with SARS-CoV-2


title: ART Patient 02 ATACseq Central memory CD4 T cells (1)


title: Metformin-2DG-Activated-3hr-donor-207_S10

value: Activated


title: TG_A

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the G. biloba genome database downloaded from GigaDB using TopHat2 software with default parameters.
Gene abundances were quantified by RSEM, and the gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcriptper Million mapped reads) method.
Genome_build: GigaDB (http://gigadb.org/dataset/100209).
Supplementary_files_format_and_content: The tab-delimited text file include FPKM vaules of genes for each sample (gene_id, CG_A_fpkm, CG_B_fpkm,, CG_C_fpkm,, TG_A_fpkm,, TG_B_fpkm,, TG_C_fpkm)

organism: Ginkgo biloba

source_name: Treatment leaves

growth_protocol: The 5-years-old G. biloba trees (‘Fozhi’ cultivar) grown at the leaf-harvesting G. biloba nursery were used in this study, with sufficient light, well-drained and fertile soil, a fixed row spacing (0.6 m × 0.6 m).

extract_protocol:
The leaves of control and truncation treatment were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 30 well-grown trees were cut into the short trunk at 85 cm height from the ground, and another 30  plants were regarded as control (without treatment).

value: truncation treatment (85 cm) leaves at leaf-harvesing stage

tag: organ

value: leaves


title: ART Patient 01 ATACseq Total CD4 T cells (1)

source_name: Total CD4 T cells

value: ART Patient 01

value: peripheral blood

value: Total CD4 T cells


title: CM2-2w

value: Before SARS-CoV-2 infection


title: CM1-3d


title: Activated-24hr-control-donor-207_S4

value: Water


title: ART Patient 01 ATACseq Total CD4 T cells (2)


title: CM1-2w


title: xpo4-2 cpr5_3

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: TAIR 10
Supplementary_files_format_and_content: raw counts and normalized abundance measurements

organism: Arabidopsis thaliana

source_name: xpo4-2 cpr5 double mutant_whole seedling

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 10-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: xpo4-2 cpr5 double mutant

value: whole seedlings


title: Activated-24hr-control-donor-44_S1

city: Cambridge

value: CD4+ T cells


title: Metformin-2DG-Activated-3hr-donor-44_S8

value: Metformin, 2-DG


title: TG_C


title: ART Patient 01 ATACseq TEMRA CD4 T cells (1)

growth_protocol: Ex vivo PBMC from different patient cohorts were directed sorted and used for NGS.

treatment_protocol: There is no treatment for patient samples.

value: TEMRA CD4 T cells


title: Activated-9hr-control-donor-44_S15


title: siUPF1 rep1

city: EDINBURGH

first: Kathryn

last: Jackson-Jones

address: Institute of Genetics and Molecular Medicine, Crewe Road South

institute: University of Edinburgh

source_name: HeLa cells

tag: cell line

value: HeLa

tag: knockdown


title: CG_B

source_name: Control leaves

tag: treatment

value: control leaves at leaf-harvesing stage


title: CG_A