title: IL-4/IL-13+TNF L49554_M2_TNF_2_05_K15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 93-Enroll

status: Public on Jan 11 2022

type: SRA

city: Hershey

first: Steven

last: Hicks

state: Pennsylvania

address: 500 University Drive

department: Pediatrics

country: USA

institute: Penn State College of Medicine

library_source: transcriptomic

data_processing:
Basecalling in Illumina BaseSpace
Adapter trimming with CUTADAPT in Partek Flow
Aligned to human genome with Bowtie2 in Partek Flow
Mature miRNAs quantified with miRBase v22
Raw counts were median normalized and mean-center scaled
Genome_build: hg38
Supplementary_files_format_and_content: csv file including normalized mature microRNA levels

molecule: total RNA

organism: Homo sapiens

source_name: Milk

extract_protocol:
Samples were spun for 20 min at 4 °C at 800 rpm to 130 separate lipid, skim, and cellular fractions. For each sample, 50 μl of the lipid fraction was used for RNA extraction. RNA purification was performed using a 134 Norgen Circulating and Exosomal RNA Purification Kit (Norgen Biotech; Ontario, Canada)
Illumina TruSeq Small RNA Prep protocol

tag: tissue

value: Milk

tag: biologic sex

value: Female

tag: maternal age

tag: race

value: Other


title: 94-Enroll

value: White


title: 92-Enroll


title: IL-4/IL-13+TNF L49542_M2_TNF_2_05_K03

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

data_processing:
Bbasecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
Read alignment: Fragments were aligned to the mouse reference genome mm10 using the aligner gsnap (2019-06-10) with Ensembl 98 splice sites as support (parameters: --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0  --action-if-cigar-error noprint).
Counts per feature: Uniquely mapped fragments were compared based on their overlap to Ensembl 98 gene annotations using featureCounts (v1.6.3) to create a table of counts per gene and cell (parameters:  -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o bfx1341.mm10.e98.txt -Q 1).
Samples were processed and analyzed in R (4.0.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells.

organism: Mus musculus

source_name: Bone marrow

growth_protocol: In the presence of M-CSF

extract_protocol:
Wild-type BMDMs were stimulated with 10ng/ml IL4, IL13 and TNF. Cells were scraped and stained for live/dead staining with LDFA. Single cells were flow-sorted into 384-well plates containing nuclease-free water with 0.2% Triton X-100 and 1 U murine RNase inhibitor, centrifuged, and frozen at −80°C. After thawing, the primer mix and 1 U murine RNase inhibitor was added to each well. The reverse transcription reaction was performed, cDNA was amplified and purified. The concentration of samples was measured using a plate reader (Infinite 200 PRO, Tecan).
Then, pre-amplified cDNA was used for library preparation (TruePrep DNA library preparation kit V2 for Illumina, Vazyme) in a 1-μL reaction volume. Illumina indices were added during the PCR reaction with 1 × KAPA Hifi HotStart Ready Mix and dual indexing primers. After PCR, the libraries were quantified with AccuBlue Broad Range kit, pooled in equimolar amounts, and purified twice with Sera-Mag SpeedBeads. The libraries were sequenced on the Novaseq 6000 Illumina platform to obtain 50 bp paired-end reads aiming at an average sequencing depth of 0.5 million reads per cell.
Single Cell RNA seq

treatment_protocol: 10ng/ml IL4, IL13 and/or TNF

tag: strain

tag: cell type

value: BMDM

tag: treatment


title: IL-4/IL-13+TNF L49541_M2_TNF_2_05_K02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 91-Enroll


title: IL-4/IL-13+TNF L49539_M2_TNF_2_05_J24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49540_M2_TNF_2_05_K01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49538_M2_TNF_2_05_J23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 90-Enroll


title: IL-4/IL-13+TNF L49537_M2_TNF_2_05_J22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49536_M2_TNF_2_05_J21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 89-Enroll

value: Asian


title: 87-Enroll


title: IL-4/IL-13+TNF L49535_M2_TNF_2_05_J20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 86-Enroll


title: IL-4/IL-13+TNF L49534_M2_TNF_2_05_J19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49533_M2_TNF_2_05_J18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49532_M2_TNF_2_05_J17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 84-Enroll


title: 85-Enroll


title: 83-Enroll


title: IL-4/IL-13+TNF L49530_M2_TNF_2_05_J15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49531_M2_TNF_2_05_J16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 82-Enroll


title: 81-Enroll


title: IL-4/IL-13+TNF L49529_M2_TNF_2_05_J14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 80-Enroll


title: IL-4/IL-13+TNF L49528_M2_TNF_2_05_J13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 79-Enroll


title: IL-4/IL-13+TNF L49526_M2_TNF_2_05_J11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 78-Enroll


title: IL-4/IL-13+TNF L49525_M2_TNF_2_05_J10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49524_M2_TNF_2_05_J09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 75-Enroll


title: 77-Enroll


title: IL-4/IL-13+TNF L49523_M2_TNF_2_05_J08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 74-Enroll


title: 71-Enroll

value: Black


title: 69-Enroll


title: 65-Enroll


title: IL-4/IL-13+TNF L49520_M2_TNF_2_05_J05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49521_M2_TNF_2_05_J06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49519_M2_TNF_2_05_J04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49522_M2_TNF_2_05_J07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 64-Enroll


title: IL-4/IL-13+TNF L49518_M2_TNF_2_05_J03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 63-Enroll


title: 61-Enroll


title: IL-4/IL-13+TNF L49516_M2_TNF_2_05_J01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 59-Enroll


title: IL-4/IL-13+TNF L49515_M2_TNF_2_05_I24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49514_M2_TNF_2_05_I23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 57-Enroll


title: 54-Enroll


title: IL-4/IL-13+TNF L49513_M2_TNF_2_05_I22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49527_M2_TNF_2_05_J12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 76-Enroll


title: IL-4/IL-13+TNF L49512_M2_TNF_2_05_I21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 53-Enroll


title: 52-Enroll


title: IL-4/IL-13+TNF L49509_M2_TNF_2_05_I18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49510_M2_TNF_2_05_I19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 49-Enroll


title: IL-4/IL-13+TNF L49511_M2_TNF_2_05_I20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49508_M2_TNF_2_05_I17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 47-Enroll


title: IL-4/IL-13+TNF L49506_M2_TNF_2_05_I15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 45-Enroll


title: IL-4/IL-13+TNF L49505_M2_TNF_2_05_I14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 48-Enroll


title: 44-Enroll


title: IL-4/IL-13+TNF L49517_M2_TNF_2_05_J02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49503_M2_TNF_2_05_I12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49502_M2_TNF_2_05_I11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 43-Enroll


title: 58-Enroll


title: IL-4/IL-13+TNF L49501_M2_TNF_2_05_I10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 41-Enroll


title: IL-4/IL-13+TNF L49500_M2_TNF_2_05_I09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 40-Enroll


title: IL-4/IL-13+TNF L49499_M2_TNF_2_05_I08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 39-Enroll


title: IL-4/IL-13+TNF L49498_M2_TNF_2_05_I07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 51-Enroll


title: 37-Enroll


title: IL-4/IL-13+TNF L49497_M2_TNF_2_05_I06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 36-Enroll


title: IL-4/IL-13+TNF L49496_M2_TNF_2_05_I05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 35-Enroll


title: IL-4/IL-13+TNF L49495_M2_TNF_2_05_I04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 34-Enroll


title: IL-4/IL-13+TNF L49507_M2_TNF_2_05_I16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 33-Enroll


title: 46-Enroll


title: IL-4/IL-13+TNF L49494_M2_TNF_2_05_I03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 32-Enroll

value: Bi-racial


title: IL-4/IL-13+TNF L49492_M2_TNF_2_05_I01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49504_M2_TNF_2_05_I13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49493_M2_TNF_2_05_I02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49299_M2_TNF_2_04_P24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 29-Enroll


title: IL-4/IL-13+TNF L49298_M2_TNF_2_04_P23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 28-Enroll


title: IL-4/IL-13+TNF L49297_M2_TNF_2_04_P22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 42-Enroll


title: IL-4/IL-13+TNF L49296_M2_TNF_2_04_P21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 24-Enroll


title: IL-4/IL-13+TNF L49294_M2_TNF_2_04_P19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 22-Enroll


title: IL-4/IL-13+TNF L49293_M2_TNF_2_04_P18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 25-Enroll


title: IL-4/IL-13+TNF L49295_M2_TNF_2_04_P20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 21-Enroll


title: IL-4/IL-13+TNF L49292_M2_TNF_2_04_P17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 20-Enroll


title: IL-4/IL-13+TNF L49291_M2_TNF_2_04_P16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 19-Enroll


title: IL-4/IL-13+TNF L49290_M2_TNF_2_04_P15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 18-Enroll


title: 30-Enroll


title: IL-4/IL-13+TNF L49289_M2_TNF_2_04_P14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 17-Enroll


title: 14-Enroll


title: 15-Enroll


title: IL-4/IL-13+TNF L49288_M2_TNF_2_04_P13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49287_M2_TNF_2_04_P12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49286_M2_TNF_2_04_P11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49285_M2_TNF_2_04_P10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 27-Enroll


title: 13-Enroll


title: IL-4/IL-13+TNF L49284_M2_TNF_2_04_P09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 11-Enroll


title: IL-4/IL-13+TNF L49282_M2_TNF_2_04_P07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49280_M2_TNF_2_04_P05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49283_M2_TNF_2_04_P08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 9-Enroll


title: IL-4/IL-13+TNF L49281_M2_TNF_2_04_P06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 7-Enroll


title: 10-Enroll


title: 6-Enroll


title: IL-4/IL-13+TNF L49275_M2_TNF_2_04_O24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49274_M2_TNF_2_04_O23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 8-Enroll


title: 16-Enroll


title: 4-Enroll


title: IL-4/IL-13+TNF L49272_M2_TNF_2_04_O21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 3-Enroll


title: 12-Enroll


title: IL-4/IL-13+TNF L49271_M2_TNF_2_04_O20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 2-Enroll


title: 1-Enroll


title: IL-4/IL-13+TNF L49268_M2_TNF_2_04_O17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49270_M2_TNF_2_04_O19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 45-Enroll-correct


title: IL-4/IL-13+TNF L49279_M2_TNF_2_04_P04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 221-4mo


title: IL-4/IL-13+TNF L49267_M2_TNF_2_04_O16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49269_M2_TNF_2_04_O18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49266_M2_TNF_2_04_O15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 5-Enroll


title: 219-4mo


title: IL-4/IL-13+TNF L49273_M2_TNF_2_04_O22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49263_M2_TNF_2_04_O12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49264_M2_TNF_2_04_O13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 216-4mo


title: 217-4mo


title: 218-4mo


title: IL-4/IL-13+TNF L49261_M2_TNF_2_04_O10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49265_M2_TNF_2_04_O14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 214-4mo


title: IL-4/IL-13+TNF L49260_M2_TNF_2_04_O09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49262_M2_TNF_2_04_O11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49259_M2_TNF_2_04_O08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 211-4mo


title: IL-4/IL-13+TNF L49258_M2_TNF_2_04_O07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 210-4mo


title: 220-4mo


title: 207-4mo


title: 204-4mo


title: IL-4/IL-13+TNF L49256_M2_TNF_2_04_O05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49255_M2_TNF_2_04_O04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 203-4mo


title: IL-4/IL-13+TNF L49254_M2_TNF_2_04_O03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49253_M2_TNF_2_04_O02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 215-4mo


title: 199-4mo


title: IL-4/IL-13+TNF L49252_M2_TNF_2_04_O01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 200-4mo


title: 196-4mo


title: 198-4mo


title: IL-4/IL-13+TNF L49250_M2_TNF_2_04_N23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49249_M2_TNF_2_04_N22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 194-4mo


title: IL-4/IL-13+TNF L49251_M2_TNF_2_04_N24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49248_M2_TNF_2_04_N21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 190-4mo


title: IL-4/IL-13+TNF L49247_M2_TNF_2_04_N20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 191-4mo


title: 213-4mo


title: 189-4mo


title: IL-4/IL-13+TNF L49245_M2_TNF_2_04_N18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 186-4mo


title: IL-4/IL-13+TNF L49257_M2_TNF_2_04_O06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49244_M2_TNF_2_04_N17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 184-4mo


title: 183-4mo


title: 181-4mo


title: 202-4mo


title: 179-4mo


title: 180-4mo


title: 177-4mo


title: 176-4mo


title: 172-4mo


title: 102-4Mo


title: IL-4/IL-13+TNF L49246_M2_TNF_2_04_N19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 96-4Mo


title: 175-4mo


title: 174-4mo


title: IL-4/IL-13+TNF L49243_M2_TNF_2_04_N16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49242_M2_TNF_2_04_N15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 86-4Mo


title: 87-4Mo


title: IL-4/IL-13+TNF L49232_M2_TNF_2_04_N05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49231_M2_TNF_2_04_N04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49238_M2_TNF_2_04_N11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49235_M2_TNF_2_04_N08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49233_M2_TNF_2_04_N06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49241_M2_TNF_2_04_N14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49240_M2_TNF_2_04_N13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49236_M2_TNF_2_04_N09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49237_M2_TNF_2_04_N10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49239_M2_TNF_2_04_N12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 159-4Mo


title: 82-4Mo


title: IL-4/IL-13+TNF L49226_M2_TNF_2_04_M23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49227_M2_TNF_2_04_M24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49228_M2_TNF_2_04_N01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 98-4Mo


title: IL-4/IL-13+TNF L49230_M2_TNF_2_04_N03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 173-4mo


title: IL-4/IL-13+TNF L49225_M2_TNF_2_04_M22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 81-4Mo


title: 84-4Mo


title: IL-4/IL-13+TNF L49222_M2_TNF_2_04_M19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49224_M2_TNF_2_04_M21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 79-4Mo


title: IL-4/IL-13+TNF L49223_M2_TNF_2_04_M20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49229_M2_TNF_2_04_N02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 78-4Mo


title: 76-4Mo


title: 67-4Mo


title: IL-4/IL-13+TNF L49218_M2_TNF_2_04_M15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49217_M2_TNF_2_04_M14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 61-4Mo


title: IL-4/IL-13+TNF L49213_M2_TNF_2_04_M10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49221_M2_TNF_2_04_M18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49220_M2_TNF_2_04_M17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 75-4Mo


title: 77-4Mo


title: IL-4/IL-13+TNF L49219_M2_TNF_2_04_M16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 63-4Mo


title: IL-4/IL-13+TNF L49216_M2_TNF_2_04_M13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 65-4Mo


title: 56-4Mo


title: 59-4Mo


title: IL-4/IL-13+TNF L49234_M2_TNF_2_04_N07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49214_M2_TNF_2_04_M11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 54-4Mo


title: IL-4/IL-13+TNF L49215_M2_TNF_2_04_M12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49210_M2_TNF_2_04_M07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 53-4Mo


title: 51-4Mo


title: IL-4/IL-13+TNF L49209_M2_TNF_2_04_M06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49206_M2_TNF_2_04_M03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 80-4Mo


title: IL-4/IL-13+TNF L49207_M2_TNF_2_04_M04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49208_M2_TNF_2_04_M05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 48-4Mo


title: IL-4/IL-13+TNF L49212_M2_TNF_2_04_M09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49211_M2_TNF_2_04_M08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 57-4Mo


title: IL-4/IL-13+TNF L49205_M2_TNF_2_04_M02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 58-4Mo


title: 49-4Mo


title: 47-4Mo


title: IL-4/IL-13+TNF L49204_M2_TNF_2_04_M01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49203_M2_TNF_2_04_L24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 45-4Mo


title: 46-4Mo


title: IL-4/IL-13+TNF L49202_M2_TNF_2_04_L23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 44-4Mo


title: IL-4/IL-13+TNF L49200_M2_TNF_2_04_L21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 42-4Mo


title: IL-4/IL-13+TNF L49201_M2_TNF_2_04_L22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49198_M2_TNF_2_04_L19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49197_M2_TNF_2_04_L18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 41-4Mo


title: IL-4/IL-13+TNF L49199_M2_TNF_2_04_L20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 37-4Mo


title: IL-4/IL-13+TNF L49196_M2_TNF_2_04_L17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 39-4Mo


title: 36-4Mo


title: 35-4Mo


title: 34-4Mo


title: 32-4Mo


title: IL-4/IL-13+TNF L49195_M2_TNF_2_04_L16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 30-4Mo


title: IL-4/IL-13+TNF L49191_M2_TNF_2_04_L12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49193_M2_TNF_2_04_L14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49192_M2_TNF_2_04_L13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49189_M2_TNF_2_04_L10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49194_M2_TNF_2_04_L15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 43-4Mo


title: 29-4Mo


title: 28-4Mo


title: 27-4Mo


title: IL-4/IL-13+TNF L49188_M2_TNF_2_04_L09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 26-4Mo


title: 40-4Mo


title: IL-4/IL-13+TNF L49186_M2_TNF_2_04_L07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 24-4Mo


title: IL-4/IL-13+TNF L49183_M2_TNF_2_04_L04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49187_M2_TNF_2_04_L08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49182_M2_TNF_2_04_L03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 21-4Mo


title: IL-4/IL-13+TNF L49184_M2_TNF_2_04_L05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 25-4Mo


title: IL-4/IL-13+TNF L49190_M2_TNF_2_04_L11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49181_M2_TNF_2_04_L02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 19-4Mo


title: 18-4Mo


title: 20-4Mo


title: 17-4Mo


title: IL-4/IL-13+TNF L49180_M2_TNF_2_04_L01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49179_M2_TNF_2_04_K24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 16-4Mo


title: 15-4Mo


title: 14-4Mo


title: IL-4/IL-13+TNF L49177_M2_TNF_2_04_K22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49176_M2_TNF_2_04_K21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49185_M2_TNF_2_04_L06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 12-4Mo


title: 13-4Mo


title: IL-4/IL-13+TNF L49175_M2_TNF_2_04_K20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49174_M2_TNF_2_04_K19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 11-4Mo


title: IL-4/IL-13+TNF L49171_M2_TNF_2_04_K16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49172_M2_TNF_2_04_K17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 8-4Mo


title: IL-4/IL-13+TNF L49173_M2_TNF_2_04_K18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 10-4Mo


title: 7-4Mo


title: IL-4/IL-13+TNF L49170_M2_TNF_2_04_K15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 5-4Mo


title: 3-4Mo


title: 4-4Mo


title: IL-4/IL-13+TNF L49167_M2_TNF_2_04_K12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49168_M2_TNF_2_04_K13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49169_M2_TNF_2_04_K14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 2-4Mo


title: IL-4/IL-13+TNF L49178_M2_TNF_2_04_K23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 1-4Mo


title: 147-1Mo


title: 144-1Mo


title: IL-4/IL-13+TNF L49164_M2_TNF_2_04_K09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49165_M2_TNF_2_04_K10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49166_M2_TNF_2_04_K11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 142-1Mo


title: IL-4/IL-13+TNF L49163_M2_TNF_2_04_K08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 133-1Mo


title: IL-4/IL-13+TNF L49162_M2_TNF_2_04_K07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 128-1Mo


title: 116-1Mo


title: 135-1Mo


title: IL-4/IL-13+TNF L49161_M2_TNF_2_04_K06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49160_M2_TNF_2_04_K05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49158_M2_TNF_2_04_K03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 106-1Mo


title: IL-4/IL-13+TNF L49156_M2_TNF_2_04_K01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49159_M2_TNF_2_04_K04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 123-1Mo


title: 105-1Mo


title: IL-4/IL-13+TNF L49157_M2_TNF_2_04_K02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49155_M2_TNF_2_04_J24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49153_M2_TNF_2_04_J22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 145-1Mo


title: IL-4/IL-13+TNF L49154_M2_TNF_2_04_J23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49152_M2_TNF_2_04_J21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 97-1Mo


title: 98-1Mo


title: 102-1Mo


title: 100-1Mo


title: IL-4/IL-13+TNF L48773_M2_TNF_1_03_K02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48775_M2_TNF_1_03_K04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 95-1Mo


title: 94-1Mo


title: IL-4/IL-13+TNF L48774_M2_TNF_1_03_K03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48771_M2_TNF_1_03_J24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 92-1Mo


title: IL-4/IL-13+TNF L49150_M2_TNF_2_04_J19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 91-1Mo


title: IL-4/IL-13+TNF L48768_M2_TNF_1_03_J21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 90-1Mo


title: IL-4/IL-13+TNF L48772_M2_TNF_1_03_K01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 86-1Mo


title: 104-1Mo


title: IL-4/IL-13+TNF L48770_M2_TNF_1_03_J23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48765_M2_TNF_1_03_J18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 85-1Mo


title: IL-4/IL-13+TNF L48764_M2_TNF_1_03_J17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 96-1Mo


title: IL-4/IL-13+TNF L48766_M2_TNF_1_03_J19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49151_M2_TNF_2_04_J20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48767_M2_TNF_1_03_J20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48762_M2_TNF_1_03_J15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 82-1Mo


title: 103-1Mo


title: 81-1Mo


title: 79-1Mo


title: IL-4/IL-13+TNF L48761_M2_TNF_1_03_J14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48759_M2_TNF_1_03_J12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48760_M2_TNF_1_03_J13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 93-1Mo


title: 77-1Mo


title: 75-1Mo


title: 76-1Mo


title: IL-4/IL-13+TNF L48758_M2_TNF_1_03_J11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48756_M2_TNF_1_03_J09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 72-1Mo


title: IL-4/IL-13+TNF L48755_M2_TNF_1_03_J08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 71-1Mo


title: IL-4/IL-13+TNF L48754_M2_TNF_1_03_J07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 70-1Mo


title: IL-4/IL-13+TNF L48753_M2_TNF_1_03_J06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 84-1Mo


title: 68-1Mo


title: IL-4/IL-13+TNF L48751_M2_TNF_1_03_J04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 67-1Mo


title: 66-1Mo


title: 65-1Mo


title: 80-1Mo


title: IL-4/IL-13+TNF L48750_M2_TNF_1_03_J03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 63-1Mo


title: IL-4/IL-13+TNF L48748_M2_TNF_1_03_J01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48747_M2_TNF_1_03_I24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 61-1Mo


title: 60-1Mo


title: IL-4/IL-13+TNF L48757_M2_TNF_1_03_J10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48745_M2_TNF_1_03_I22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 58-1Mo


title: IL-4/IL-13+TNF L48744_M2_TNF_1_03_I21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 57-1Mo


title: IL-4/IL-13+TNF L48743_M2_TNF_1_03_I20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 56-1Mo


title: IL-4/IL-13+TNF L48742_M2_TNF_1_03_I19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 54-1Mo


title: 53-1Mo


title: IL-4/IL-13+TNF L48740_M2_TNF_1_03_I17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48741_M2_TNF_1_03_I18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48739_M2_TNF_1_03_I16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 51-1Mo


title: IL-4/IL-13+TNF L48752_M2_TNF_1_03_J05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48738_M2_TNF_1_03_I15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48737_M2_TNF_1_03_I14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 48-1Mo


title: IL-4/IL-13+TNF L48749_M2_TNF_1_03_J02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 47-1Mo


title: 46-1Mo


title: IL-4/IL-13+TNF L48746_M2_TNF_1_03_I23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 45-1Mo


title: 59-1Mo


title: IL-4/IL-13+TNF L48735_M2_TNF_1_03_I12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48736_M2_TNF_1_03_I13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48734_M2_TNF_1_03_I11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48733_M2_TNF_1_03_I10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 42-1Mo


title: IL-4/IL-13+TNF L48732_M2_TNF_1_03_I09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48731_M2_TNF_1_03_I08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 49-1Mo


title: 41-1Mo


title: IL-4/IL-13+TNF L48730_M2_TNF_1_03_I07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48729_M2_TNF_1_03_I06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 40-1Mo


title: 39-1Mo


title: IL-4/IL-13+TNF L48727_M2_TNF_1_03_I04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 89-1Mo


title: 37-1Mo


title: IL-4/IL-13+TNF L48728_M2_TNF_1_03_I05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 36-1Mo


title: IL-4/IL-13+TNF L48726_M2_TNF_1_03_I03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 34-1Mo


title: 35-1Mo


title: IL-4/IL-13+TNF L48725_M2_TNF_1_03_I02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48724_M2_TNF_1_03_I01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 44-1Mo


title: IL-4/IL-13+TNF L48529_M2_TNF_1_02_P22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48528_M2_TNF_1_02_P21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 32-1Mo


title: 43-1Mo


title: 33-1Mo


title: 29-1Mo


title: IL-4/IL-13+TNF L48530_M2_TNF_1_02_P23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48531_M2_TNF_1_02_P24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 30-1Mo


title: 28-1Mo


title: IL-4/IL-13+TNF L48526_M2_TNF_1_02_P19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 27-1Mo


title: IL-4/IL-13+TNF L48763_M2_TNF_1_03_J16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 25-1Mo


title: IL-4/IL-13+TNF L48525_M2_TNF_1_02_P18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 24-1Mo


title: IL-4/IL-13+TNF L48524_M2_TNF_1_02_P17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48523_M2_TNF_1_02_P16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 21-1Mo


title: IL-4/IL-13+TNF L48522_M2_TNF_1_02_P15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 20-1Mo


title: IL-4/IL-13+TNF L48521_M2_TNF_1_02_P14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 19-1Mo


title: 17-1Mo


title: 18-1Mo


title: IL-4/IL-13+TNF L48518_M2_TNF_1_02_P11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48519_M2_TNF_1_02_P12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 16-1Mo


title: IL-4/IL-13+TNF L48517_M2_TNF_1_02_P10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48520_M2_TNF_1_02_P13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48527_M2_TNF_1_02_P20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48514_M2_TNF_1_02_P07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 15-1Mo


title: IL-4/IL-13+TNF L48515_M2_TNF_1_02_P08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48516_M2_TNF_1_02_P09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48769_M2_TNF_1_03_J22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 11-1Mo


title: 10-1Mo


title: IL-4/IL-13+TNF L48512_M2_TNF_1_02_P05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 26-1Mo


title: 12-1Mo


title: IL-4/IL-13+TNF L48513_M2_TNF_1_02_P06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 9-1Mo


title: IL-4/IL-13+TNF L48511_M2_TNF_1_02_P04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 8-1Mo


title: 7-1Mo


title: IL-4/IL-13+TNF L48506_M2_TNF_1_02_O23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48505_M2_TNF_1_02_O22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 6-1Mo


title: 5-1Mo


title: 13-1Mo


title: 4-1Mo


title: IL-4/IL-13+TNF L48504_M2_TNF_1_02_O21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48503_M2_TNF_1_02_O20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 2-1Mo


title: 1-1Mo


title: 3-1Mo


title: RNA_rep1_TP72hr

city: Piscataway

first: Anat

last: Kreimer

state: NJ

address: 679 Hoes Ln W

department: CABM

institute: Rutgers University

description:
rnaAnnot.tsv
rnaCounts.tsv
new_uq_alphas.csv
Combined_full_res.csv

data_processing:
Library strategy: MPRA
We used the MPRAflow (Nature Protocols 2020) pipeline to associate barcodes to assayed sequences and count barcodes per sequence
We used the MPRAnalyze (Genome Biology 2019) pipeline to detect regulatory activity of sequences and identify motifs effects in the tested regions
Supplementary_files_format_and_content: association.tsv (The 15bp barcode sequence associated with each designed sequence)
Supplementary_files_format_and_content: dnaAnnot.tsv (DNA annotations across time points, replicate and barcodes)
Supplementary_files_format_and_content: dnaCounts.tsv (DNA barcode counts for each sequence ( per time point, replicate and barcode))
Supplementary_files_format_and_content: rnaAnnot.tsv (RNA annotations across time points, replicate and barcodes)
Supplementary_files_format_and_content: rnaCounts.tsv (RNA barcode counts for each sequence ( per time point, replicate and barcode))
Supplementary_files_format_and_content: new_uq_alphas.csv (alpha per sequence (from MPRAnalyze))
Supplementary_files_format_and_content: Combined_full_res.csv (Log2FC when comparing perturbation to WT (from MPRAnalyze))

source_name: H1 hESC-derived neural progenitor cells TP72hr

growth_protocol: H1 hESCs were culture in mTeSR1 media on matrigel coated dishes.

extract_protocol:
Cell nuclei were isolated as described previously (Buenrostro et al., 2013), lysed in RLT plus buffer (Qiagen) and stored at -80C. Genomic DNA and RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen).
12ug RNA and reverse-transcribed using SuperscriptII. The cDNA and 12 ug genomic DNA were used for PCR. PCR products were size-selected with an agarose gel, purified with AmPure XP beads (Beckman coulter) and pooled.
DNA-seq, RNA-seq

treatment_protocol: hESCs were infected with the lentiMPRA library and incubated for 3 days, followed by neural induction with dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.

value: H1 hESC-derived neural progenitor cells

tag: time


title: RNA_rep2_TP72hr


title: DNA_rep3_TP72hr

description:
dnaAnnot.tsv
dnaCounts.tsv
new_uq_alphas.csv
Combined_full_res.csv

library_source: genomic

molecule: genomic DNA


title: IL-4/IL-13+TNF L48507_M2_TNF_1_02_O24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48499_M2_TNF_1_02_O16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48501_M2_TNF_1_02_O18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48500_M2_TNF_1_02_O17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48497_M2_TNF_1_02_O14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48498_M2_TNF_1_02_O15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48496_M2_TNF_1_02_O13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep2_TP72hr


title: DNA_rep1_TP72hr


title: IL-4/IL-13+TNF L48502_M2_TNF_1_02_O19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48493_M2_TNF_1_02_O10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48495_M2_TNF_1_02_O12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48494_M2_TNF_1_02_O11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48490_M2_TNF_1_02_O07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48489_M2_TNF_1_02_O06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep3_TP72hr


title: IL-4/IL-13+TNF L48491_M2_TNF_1_02_O08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep2_TP48hr

source_name: H1 hESC-derived neural progenitor cells TP48hr


title: RNA_rep1_TP48hr


title: IL-4/IL-13+TNF L48488_M2_TNF_1_02_O05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep3_TP48hr


title: IL-4/IL-13+TNF L48487_M2_TNF_1_02_O04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep3_TP48hr


title: IL-4/IL-13+TNF L48486_M2_TNF_1_02_O03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48485_M2_TNF_1_02_O02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep1_TP48hr


title: RNA_rep1_TP24hr

source_name: H1 hESC-derived neural progenitor cells TP24hr


title: DNA_rep2_TP48hr


title: RNA_rep3_TP24hr


title: DNA_rep3_TP24hr


title: DNA_rep1_TP24hr


title: RNA_rep3_TP12hr

source_name: H1 hESC-derived neural progenitor cells TP12hr


title: DNA_rep2_TP24hr


title: IL-4/IL-13+TNF L48483_M2_TNF_1_02_N24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48482_M2_TNF_1_02_N23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48492_M2_TNF_1_02_O09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48484_M2_TNF_1_02_O01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep2_TP12hr


title: IL-4/IL-13+TNF L48479_M2_TNF_1_02_N20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48481_M2_TNF_1_02_N22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48480_M2_TNF_1_02_N21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep3_TP12hr


title: IL-4/IL-13+TNF L48477_M2_TNF_1_02_N18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48478_M2_TNF_1_02_N19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep2_TP12hr


title: RNA_rep2_TP24hr


title: IL-4/IL-13+TNF L48476_M2_TNF_1_02_N17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep3_TP6hr

source_name: H1 hESC-derived neural progenitor cells TP6hr


title: RNA_rep1_TP12hr


title: RNA_rep2_TP6hr


title: IL-4/IL-13+TNF L48474_M2_TNF_1_02_N15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep3_TP6hr


title: DNA_rep1_TP6hr


title: DNA_rep2_TP6hr


title: IL-4/IL-13+TNF L48471_M2_TNF_1_02_N12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48473_M2_TNF_1_02_N14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48475_M2_TNF_1_02_N16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48472_M2_TNF_1_02_N13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48470_M2_TNF_1_02_N11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48469_M2_TNF_1_02_N10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep3_TP3hr

source_name: H1 hESC-derived neural progenitor cells TP3hr


title: IL-4/IL-13+TNF L48467_M2_TNF_1_02_N08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48466_M2_TNF_1_02_N07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep1_TP3hr


title: IL-4/IL-13+TNF L48468_M2_TNF_1_02_N09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep2_TP3hr


title: IL-4/IL-13+TNF L48464_M2_TNF_1_02_N05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep1_TP12hr


title: IL-4/IL-13+TNF L48465_M2_TNF_1_02_N06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep1_TP3hr


title: RNA_rep2_TP0hr

source_name: H1 hESC-derived neural progenitor cells TP0hr


title: IL-4/IL-13+TNF L48462_M2_TNF_1_02_N03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep1_TP0hr


title: IL-4/IL-13+TNF L48463_M2_TNF_1_02_N04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48461_M2_TNF_1_02_N02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep1_TP6hr


title: DNA_rep3_TP0hr


title: DNA_rep2_TP0hr


title: IL-4/IL-13+TNF L48459_M2_TNF_1_02_M24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48460_M2_TNF_1_02_N01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep2_TP3hr


title: DNA_rep3_TP3hr


title: IL-4/IL-13+TNF L48458_M2_TNF_1_02_M23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: DNA_rep1_TP0hr


title: IL-4/IL-13+TNF L48457_M2_TNF_1_02_M22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48456_M2_TNF_1_02_M21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: MEG8 Gapmer rep 4

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads of at least 15 nucleotides were cleared for subsequent analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Only genes with a minimum fold change of +- 1.5 (log2 +-0.585), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed
Genome_build: hg38
Supplementary_files_format_and_content: library-size normalized counts

source_name: Umbilical vein endothelial cells

growth_protocol: Cells were cultured in endothelial cell medium (Sciencell) including 10% FBS, ECGF and p/s

extract_protocol:
RNA was extracted using the Direct Zol RNA extraction kit from Zymo. RNA was dissolved in dH2O and snap frozen in liquid nitrogen
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

treatment_protocol: Gapmers were tranfected using Optimem Glutamax and lipofectamine RNAiMax. After 4 hours, transfection mix was replaced by complete culture medium. RNA was collected 48 hours after transfection

tag: passage

value: Endothelial cells


title: MEG8 Gapmer rep 1


title: MEG8 Gapmer rep 3


title: MEG8 Gapmer rep 2


title: Control Gapmer rep 3


title: IL-4/IL-13+TNF L48453_M2_TNF_1_02_M18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48454_M2_TNF_1_02_M19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48455_M2_TNF_1_02_M20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: RNA_rep3_TP0hr


title: Control Gapmer rep 2


title: Control Gapmer rep 1


title: IL-4/IL-13+TNF L48451_M2_TNF_1_02_M16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human subcutaneous white adipose 256-1

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

data_processing:
In Drop-Seq data, the cDNA read is single-ended (read 2); read 1 contains cell and UMI barcodes pertaining to the read
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Adjustments were made to the cell-tagging functions of this pipeline to account for the structure of the 10X barcode read: “BASE_RANGE=1-16” and “BASE_RANGE=17-28”, for the cell and UMI barcodes, respectively. The 10X TSO was provided to the starting sequence trimmer (“SEQUENCE=AAGCAGTGGTATCAACGCAGAGTACATGGG”); this is a minor deviation from the assumed TSO. Reads from were aligned with STAR (version 2.7.3) against the GRCm38 and GRCh38 genome assemblies for mouse and human, respectively. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 16 of the GENCODE mouse annotation or release 27 of the human annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse DGE matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell UMI counts.

molecule: polyA RNA

source_name: subcutaneous adipose tissue

extract_protocol:
Nuclei were isolated from frozen mouse and human adipose tissue samples for 10x snRNA-seq using a slightly modified approach to what was previously described50–52. Samples were kept frozen on dry ice until immediately before nuclei isolation, and all sample handling steps were performed on ice. Each flash-frozen adipose tissue sample was placed into a gentleMACS C tube (Miltenyi Biotec) with 2 mL freshly prepared TST buffer (0.03% Tween 20 [Bio-Rad], 0.01% Molecular Grade BSA [New England Biolabs], 146 mM NaCl [ThermoFisher Scientific], 1 mM CaCl2 [VWR International], 21 mM MgCl2 [Sigma Aldrich], and 10 mM Tris-Hcl pH 7.5 [ThermoFisher Scientific] in Ultrapure water [ThermoFisher Scientific]) with or without 0.2 U/ µL of Protector RNase Inhibitor (Sigma Aldrich). gentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec) and tissue was dissociated by running the program “mr_adipose_01” twice, and then incubated on ice for 10 minutes. Lysate was passed through a 40 µm nylon filter (CellTreat) and collected into a 50 mL conical tube (Corning). Filter was rinsed with 3 mL of freshly prepared ST buffer buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with or without 0.2 U/µL RNase Inhibitor, and collected into the same tube. Flow-through was centrifuged at 500 x g for 5 minutes at 4ºC with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 50 - 200 µl PBS pH 7.4 (ThermoFisher Scientific) with 0.02% BSA, with or without 0.2U/µL RNase Inhibitor. In order to reduce ambient mRNA, the nuclear pellets of some samples were washed 1-3 times with 5 mL of PBS-0.02% BSA before final resuspension. An aliquot of nuclei from each sample was stained with NucBlue (Thermofisher Scientific), counted in a hemocytometer using fluorescence to identify intact nuclei, and then immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol.
For each sample, 10,000-16,500 nuclei were loaded in one channel of a Chromium Chip (10x Genomics). The Single Cell 3’ v3.1 chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent).
cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina) with a 75-cycle kit and the following read structure: Read 1: 28 cycles, Read 2: 55 cycles, Index Read 1: 8 cycles.
OTHER: 10X Chromium Single-Cell 3’ (v3 Chemistry)

value: white adipose tissue

tag: Sex

value: female

tag: age

tag: bmi

tag: surgery

value: CCY


title: IL-4/IL-13+TNF L48452_M2_TNF_1_02_M17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48450_M2_TNF_1_02_M15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human subcutaneous white adipose 255-1


title: Human subcutaneous white adipose 253-1

value: TAH BSO


title: Human subcutaneous white adipose 254-1


title: IL-4/IL-13+TNF L48447_M2_TNF_1_02_M12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48449_M2_TNF_1_02_M14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48448_M2_TNF_1_02_M13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48446_M2_TNF_1_02_M11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48444_M2_TNF_1_02_M09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48445_M2_TNF_1_02_M10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human subcutaneous white adipose 04-1


title: Human subcutaneous white adipose 01-1


title: Human subcutaneous white adipose 02-1


title: Human visceral white adipose 256-1

source_name: omental adipose tissue


title: Human visceral white adipose 255-1


title: IL-4/IL-13+TNF L48442_M2_TNF_1_02_M07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human visceral white adipose 254-1

value: Hernia


title: IL-4/IL-13+TNF L48440_M2_TNF_1_02_M05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human visceral white adipose 01-1

value: VSG


title: IL-4/IL-13+TNF L48441_M2_TNF_1_02_M06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human visceral white adipose 253-1


title: IL-4/IL-13+TNF L48439_M2_TNF_1_02_M04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48438_M2_TNF_1_02_M03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48437_M2_TNF_1_02_M02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48435_M2_TNF_1_02_L24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48434_M2_TNF_1_02_L23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #249-1A-1

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Reads from were aligned with STAR (version 2.7.3) against the GRCh38 genome assembly. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 27 of the human GENCODE annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell UMI counts.

extract_protocol:
Whole tissue subcutaneous adipose specimens were freshly collected from the operating room. Skin was removed, and adipose tissue was cut into 1- to 2-inch pieces and rinsed thoroughly with 37 °C PBS to remove blood. Cleaned adipose tissue pieces were quickly minced in an electric grinder with 3/16-inch hole plate, and 400 ml of sample was placed in a 2-l wide-mouthed Erlenmeyer culture flask with 100 ml of freshly prepared blendzyme (Roche Liberase TM, research grade, cat. no. 05401127001, in PBS, at a ratio of 6.25 mg per 50 ml) and shaken in a 37 °C shaking incubator at 120 r.p.m. for 15–20 min to digest until the sample appeared uniform. Digestion was stopped with 100 ml of freshly made KRB (5.5 mM glucose, 137 mM NaCl, 15 mM HEPES, 5 mM KCl, 1.25 mM CaCl2, 0.44 mM KH2PO4, 0.34 mM Na2HPO4 and 0.8 mM MgSO4), supplemented with 2% BSA. Digested tissue was filtered through a 300 μM sieve and washed with KRB/albumin and flow through until only connective tissue remained. Samples were centrifuged at 233g for 5 min at room temperature, clear lipid was later removed, and floated adipocyte supernatant was collected, divided into aliquots and flash-frozen in liquid nitrogen. After removal of floated adipocytes, remaining supernatant was aspirated and the remaining pelleted stromal vascular fraction (SVF)was combined from multiple tubes. The combined SVF was washed 2 times with 50ml cold PBS with 233g for 5 min centrifugation between washes. Erythrocytes were depleted with two rounds of 25 ml. ACK lysing buffer (Gibco™ A1049201) exposure (5 minutes at RT followed by 233g x 5 min centrifugation). Remaining SVF pellet was further washed x 2 with 50ml cold PBS prior to counting on hematocytometer and loading onto Drop-seq microfluidic devices. Drop-seq was performed as described (Macosko et. al., 2015), with flow rates of 2.1 mL/h were used for each aqueous suspension and 12 mL/h for the oil.
Libraries were sequenced on the Illumina NextSeq 500, using between 1.6-1.7 pM in a volume of 1.2 mL HT1 and 3 mL of 0.3 μM Read1CustSeqB (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) using 20 x 8 x 60 read structure.
Drop-Seq (scRNA-Seq)

value: stromal vascular fraction of adipose tissue

value: DIEP


title: SVF of human SAT #249-2A-1


title: SVF of human SAT #249-1B-1


title: SVF of human SAT #248-2A-1

value: Panniculectomy


title: IL-4/IL-13+TNF L48436_M2_TNF_1_02_M01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48432_M2_TNF_1_02_L21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48443_M2_TNF_1_02_M08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48433_M2_TNF_1_02_L22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Human visceral white adipose 01-2


title: IL-4/IL-13+TNF L48431_M2_TNF_1_02_L20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48429_M2_TNF_1_02_L18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #248-1A-1


title: IL-4/IL-13+TNF L48430_M2_TNF_1_02_L19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #242-2B-1


title: IL-4/IL-13+TNF L48428_M2_TNF_1_02_L17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #242-3A-1


title: SVF of human SAT #242-2A-1


title: SVF of human SAT #240-1B-1


title: SVF of human SAT #239-3BC-1


title: IL-4/IL-13+TNF L48427_M2_TNF_1_02_L16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #242-1B-1


title: IL-4/IL-13+TNF L48425_M2_TNF_1_02_L14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #239-3B-1


title: IL-4/IL-13+TNF L48426_M2_TNF_1_02_L15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48424_M2_TNF_1_02_L13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #249-2B-1


title: SVF of human SAT #248-1B-1


title: IL-4/IL-13+TNF L48423_M2_TNF_1_02_L12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #239-3A-1


title: IL-4/IL-13+TNF L48420_M2_TNF_1_02_L09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #239-1A-1


title: IL-4/IL-13+TNF L48419_M2_TNF_1_02_L08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #239-2A-1


title: SVF of human SAT #239-1B-2


title: SVF of human SAT #238-2A-1

value: Abdominoplasty


title: SVF of human SAT #238-2B-1


title: IL-4/IL-13+TNF L48418_M2_TNF_1_02_L07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #238-1B-1


title: SVF of human SAT #238-1A-1


title: SVF of human SAT #237-2A-1


title: IL-4/IL-13+TNF L48416_M2_TNF_1_02_L05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48415_M2_TNF_1_02_L04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #237-1A-1


title: IL-4/IL-13+TNF L48414_M2_TNF_1_02_L03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48413_M2_TNF_1_02_L02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48412_M2_TNF_1_02_L01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #236-1A-2

value: Thighplasty


title: SVF of human SAT #236-1B-1


title: SVF of human SAT #236-1A-1


title: IL-4/IL-13+TNF L48422_M2_TNF_1_02_L11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

value: BMDM


title: SVF of human SAT #236-2A-2


title: IL-4/IL-13+TNF L48410_M2_TNF_1_02_K23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #235-2B-2


title: IL-4/IL-13+TNF L48421_M2_TNF_1_02_L10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48409_M2_TNF_1_02_K22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48408_M2_TNF_1_02_K21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #235-2B-1


title: SVF of human SAT #235-2A-2


title: IL-4/IL-13+TNF L48406_M2_TNF_1_02_K19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #235-1B-2


title: SVF of human SAT #235-2A-1


title: IL-4/IL-13+TNF L48407_M2_TNF_1_02_K20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48404_M2_TNF_1_02_K17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48417_M2_TNF_1_02_L06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #235-1A-1


title: IL-4/IL-13+TNF L48403_M2_TNF_1_02_K16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48401_M2_TNF_1_02_K14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48402_M2_TNF_1_02_K15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 215

data_processing:
Sequencing reads were demultiplexed using bcl2fastq and aligned to the GRCh37 human genome assembly.
Data was processed using the ENCODE RNA-Seq paired end pipeline (https://www.encodeproject.org/pipelines/).
R package tximport (Robinson et al., 2015) was used to get salmon TPMs from quant files.
Normalization, batch correction and differential expression analysis were performed using EdgeR (Robinson et al., 2010).
For differential gene expression analysis, we only tested genes that were detected in at least four samples with log2CPM ≥ -2.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with log2CPM gene counts for every gene and every sample.

source_name: Subcutaneous Adipose Tissue

extract_protocol:
Whole tissue subcutaneous adipose specimens were freshly collected from the operating room. Skin was removed, and adipose tissue was cut into 1- to 2-inch pieces and rinsed thoroughly with 37 °C PBS to remove blood. Cleaned adipose tissue pieces were quickly minced in an electric grinder with 3/16-inch hole plate, and 400 ml of sample was placed in a 2-l wide-mouthed Erlenmeyer culture flask with 100 ml of freshly prepared blendzyme (Roche Liberase TM, research grade, cat. no. 05401127001, in PBS, at a ratio of 6.25 mg per 50 ml) and shaken in a 37 °C shaking incubator at 120 r.p.m. for 15–20 min to digest until the sample appeared uniform. Digestion was stopped with 100 ml of freshly made KRB (5.5 mM glucose, 137 mM NaCl, 15 mM HEPES, 5 mM KCl, 1.25 mM CaCl2, 0.44 mM KH2PO4, 0.34 mM Na2HPO4 and 0.8 mM MgSO4), supplemented with 2% BSA. Digested tissue was filtered through a 300 μM sieve and washed with KRB/albumin and flow through until only connective tissue remained. Samples were centrifuged at 233g for 5 min at room temperature, clear lipid was later removed, and floated adipocyte supernatant was collected, divided into aliquots and flash-frozen in liquid nitrogen. Total RNA from ~400 μl of thawed floated adipocytes was isolated in TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
For RNA-seq library construction, mRNA was purified from 100 ng of total RNA by using a Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and convert into double-stranded complementary DNA by using an NEBNext mRNA Second Strand Synthesis Module (E6111L). cDNA was subsequently tagmented and amplified for 12 cycles by using a Nextera XT DNA Library Preparation Kit (Illumina FC-131). Sequencing libraries were analyzed with Qubit and Agilent Bioanalyzer, pooled at a final loading concentration of 1.8 pM and sequenced on a NextSeq500.

value: Adipocyte

value: F

tag: homa-ir

tag: hdl

tag: ldl

tag: tg


title: IL-4/IL-13+TNF L48411_M2_TNF_1_02_K24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48400_M2_TNF_1_02_K13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 213


title: HS SAT IS sample 214


title: IL-4/IL-13+TNF L48397_M2_TNF_1_02_K10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 203

value: L DIEP


title: IL-4/IL-13+TNF L48398_M2_TNF_1_02_K11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 188


title: IL-4/IL-13+TNF L48399_M2_TNF_1_02_K12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 170


title: HS SAT IS sample 178

value: R DIEP


title: IL-4/IL-13+TNF L48396_M2_TNF_1_02_K09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48405_M2_TNF_1_02_K18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48393_M2_TNF_1_02_K06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48395_M2_TNF_1_02_K08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48392_M2_TNF_1_02_K05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48394_M2_TNF_1_02_K07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #235-1B-1

tag: tissue


title: HS SAT IS sample 160


title: HS SAT IS sample 168


title: IL-4/IL-13+TNF L48391_M2_TNF_1_02_K04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 144


title: IL-4/IL-13+TNF L48390_M2_TNF_1_02_K03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48389_M2_TNF_1_02_K02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 141

value: Belt Lipectomy


title: HS SAT IS sample 122

value: R TRAM Flap


title: IL-4/IL-13+TNF L48386_M2_TNF_1_02_J23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: SVF of human SAT #235-1A-2

value: female


title: HS SAT IR sample 220


title: HS SAT IR sample 222


title: IL-4/IL-13+TNF L48383_M2_TNF_1_02_J20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 216


title: IL-4/IL-13+TNF L48384_M2_TNF_1_02_J21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48382_M2_TNF_1_02_J19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IS sample 134


title: HS SAT IS sample 121


title: HS SAT IS sample 157


title: HS SAT IR sample 211


title: HS SAT IR sample 212


title: IL-4/IL-13+TNF L48380_M2_TNF_1_02_J17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48381_M2_TNF_1_02_J18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 210


title: IL-4/IL-13+TNF L48379_M2_TNF_1_02_J16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 209


title: HS SAT IS sample 123


title: IL-4/IL-13+TNF L48388_M2_TNF_1_02_K01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 207


title: HS SAT IR sample 206


title: IL-4/IL-13+TNF L48387_M2_TNF_1_02_J24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48376_M2_TNF_1_02_J13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48377_M2_TNF_1_02_J14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48378_M2_TNF_1_02_J15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48385_M2_TNF_1_02_J22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 205


title: IL-4/IL-13+TNF L48374_M2_TNF_1_02_J11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48375_M2_TNF_1_02_J12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 195

value: L DIEP Flap


title: HS SAT IR sample 193

value: TRAM Flap


title: HS SAT IR sample 202


title: IL-4/IL-13+TNF L48373_M2_TNF_1_02_J10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48372_M2_TNF_1_02_J09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 190


title: IL-4/IL-13+TNF L48371_M2_TNF_1_02_J08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48369_M2_TNF_1_02_J06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48368_M2_TNF_1_02_J05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48370_M2_TNF_1_02_J07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48366_M2_TNF_1_02_J03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 180


title: IL-4/IL-13+TNF L48365_M2_TNF_1_02_J02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 172


title: HS SAT IR sample 158

value: DIEP Flap


title: IL-4/IL-13+TNF L48367_M2_TNF_1_02_J04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 163


title: HS SAT IR sample 142


title: HS SAT IR sample 137


title: HS SAT IR sample 133


title: HS SAT IR sample 130


title: IL-4/IL-13+TNF L48364_M2_TNF_1_02_J01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48363_M2_TNF_1_02_I24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48362_M2_TNF_1_02_I23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HS SAT IR sample 129


title: IL-4/IL-13+TNF L48361_M2_TNF_1_02_I22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48360_M2_TNF_1_02_I21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ INDOXIMOD 3

data_processing:
Qauklity check of the raw files using FastQC (v. 0.7.11)
After sequencing raw reads were filteredto discard reads with contaminations, low quality or adapter residues
The raw file were mapped to the human genome build GRCh38 using the STAR aligner (v. 2.7.4a)
the reads were counted per gene using the featureCounts tool from the SubRead package (v. 2.0.1)
differentail expression analysis was done using DESeq2 (v. 1.30.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HeLa cells

growth_protocol: 0.1 x10^6 HeLa cells were plated per well of a 12-well plate in DMEM medium containing 10% FBS and 1% Penicillin-Streptomycin 14 h before treatment.

extract_protocol:
RNA isolation was performed using the RNeasy mini kit from QIAGEN.
mRNA sequencing libraries were prepared from 1ug of total RNA of each sample using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7765, NEB) with NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEB) according to the manufacturer's recommendations.

treatment_protocol: The cells were treated for 24 h in triplicates per treatment with ctrl DMEM medium, DMEM with 10 ng/ml of IFNγ, DMEM with 10 ng/ml of IFNγ + 100µM indoximod, DMEM with 10 ng/ml of IFNγ + 1µM epacadostat and DMEM with 10 ng/ml of IFNγ+  1µM BMS986205.

value: 24h IFN-gamma + INDOXIMOD


title: HS SAT IR sample 199

value: Lipoabdominoplasty


title: HS SAT IR sample 124


title: HS SAT IR sample 181


title: IL-4/IL-13+TNF L48359_M2_TNF_1_02_I20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48358_M2_TNF_1_02_I19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48356_M2_TNF_1_02_I17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48357_M2_TNF_1_02_I18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ BMS986205 3

value: 24h IFN-gamma + BMS986205


title: HeLa_IFNγ INDOXIMOD 1


title: IL-4/IL-13+TNF L48355_M2_TNF_1_02_I16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ BMS986205 2


title: IL-4/IL-13+TNF L48354_M2_TNF_1_02_I15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48353_M2_TNF_1_02_I14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ EPACADOSTAT 2

value: 24h IFN-gamma + EPACADOSTAT


title: IL-4/IL-13+TNF L48351_M2_TNF_1_02_I12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ BMS986205 1


title: HeLa_IFNγ EPACADOSTAT 3


title: IL-4/IL-13+TNF L48349_M2_TNF_1_02_I10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48350_M2_TNF_1_02_I11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IDO1 ko_IFNγ 2

value: 24h IFN-gamma


title: IL-4/IL-13+TNF L48348_M2_TNF_1_02_I09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IDO1 ko_IFNγ 1


title: HeLa_IFNγ INDOXIMOD 2


title: HS SAT IR sample 120

value: DIEP


title: IL-4/IL-13+TNF L48347_M2_TNF_1_02_I08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

value: BMDM


title: IL-4/IL-13+TNF L48352_M2_TNF_1_02_I13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IDO1 ko_IFNγ 3


title: IL-4/IL-13+TNF L48345_M2_TNF_1_02_I06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48344_M2_TNF_1_02_I05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ 3


title: IL-4/IL-13+TNF L48346_M2_TNF_1_02_I07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ 5


title: HeLa_IFNγ 6


title: HeLa_IFNγ 4


title: HeLa_IFNγ 2


title: IL-4/IL-13+TNF L48343_M2_TNF_1_02_I04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48342_M2_TNF_1_02_I03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13 L49662_B_M2_05_P03

description:
IL-4/IL-13
IL-4/IL-13


title: HeLa_IFNγ 1


title: HeLa_ut 3

value: 24h ctrl


title: HeLa_ut 2


title: IL-4/IL-13+TNF L48340_M2_TNF_1_02_I01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: HeLa_IFNγ EPACADOSTAT 1


title: HeLa_ut 1


title: T24_si_3

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

data_processing:
Data were trimmed of sequencing adaptors and low quality base calls using BBDuk tool in the BBMap package. Alignment to the human hg19/GRCh37 genome reference was done using STAR version 2.5.2a23. Duplicate reads were marked using Picard MarkDuplicates. Read counts were produced by the featureCounts tool from the SubRead package24.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: markdup.featco.2.counts.txt: Raw count matrix.

source_name: Human bladder cancer cell line T24

growth_protocol: Human bladder cancer cell lines RT4 (RRID:CVCL_0036, grade 1) and T24 (RRID:CVCL_0554, grade 3) were purchased from Sigma-Aldrich (St Louis, MO, USA). The cells were cultured in McCoy’s 5a medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin in a humified 5% CO2 atmosphere at 37ºC. All reagents for the in vitro experiments were purchased from ThermoFisher Scientific (Rockford, IL, USA) unless stated otherwise.

extract_protocol:
The cell samples were thawed and RNA purification was performed using TRIzol with phasemaker tubes according to manufacturer’s instructions. RNA cleanup was performed using RNeasy minelute kit (QIAGEN) and the RNA concentration was determined using Qubit with the RNA HS kit.
RNA quantification and quality assessment were performed using Nanodrop 1000 (Mason Technology) and Bioanalyzer 2100 (Agilent). cDNA libraries were prepared from the RNA samples using TruSeq Stranded mRNA Library Prep Kit on the NeoPrep instrument (Illumina) according to manufacturer’s instructions, and sequenced (single end 1x75 bp) using the NextSeq 500 platform (Illumina).

treatment_protocol: Cells were seeded in T-25 flasks (5x10^5 cells) and incubated for 24h in 37oC. The cells were washed twice in phosphate buffered saline (PBS) and received growth medium without FBS, in addition to Lipofectamine 2000 and negative control or anti-RBM3 (s11858+s11860) siRNA in OptiMEM to a final siRNA concentration of 25 nM. The transfection was stopped after 4.5 h, medium changed to full growth medium and the cells were left to recover overnight. The following day, cells were harvested and spun down to pellets. The pellets were either fixated, dehydrated and embedded in paraffin for immunocytochemistry or resuspended in TRIzol and stored at -20oC for qPCR.

tag: cell line

value: Bladder cancer cell line

tag: grade

value: siRNA targetting RBM3


title: T24_si_4


title: T24_ctrl_3

value: Control


title: T24_ctrl_5


title: IL-4/IL-13 L49487_M2_2_05_H20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49483_M2_2_05_H16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49490_M2_2_05_H23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49486_M2_2_05_H19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49491_M2_2_05_H24

description:
IL-4/IL-13
IL-4/IL-13


title: T24_si_5


title: IL-4/IL-13 L49489_M2_2_05_H22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49485_M2_2_05_H18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49488_M2_2_05_H21

description:
IL-4/IL-13
IL-4/IL-13


title: AB8817

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: A*.txt file:  includes mRNA molecule count values for each Sample (single cell expression matrix)
metadata_q.txt:  Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: normal adjacent lung tissue

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
[human samples]  Samples of tumor and adjacent normal lung tissues were obtained from treatment-naive surgical specimens of NSCLC patients undergoing resection at the Mount Sinai Medical Center (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
(1) Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
(2) mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

tag: organ

value: normal adjacent lung tissue

value: Myeloid cells

tag: selection marker

tag: time point

tag: patient id

tag: replicate id


title: AB8818

tag: cell type

value: T cells


title: AB8819


title: IL-4/IL-13 L49481_M2_2_05_H14

description:
IL-4/IL-13
IL-4/IL-13

tag: strain

tag: treatment


title: IL-4/IL-13 L49482_M2_2_05_H15

description:
IL-4/IL-13
IL-4/IL-13


title: AB8816


title: AB8815

value: doublets of T cells and myeloid cells


title: AB8814

source_name: NSCLC tumor

value: NSCLC tumor


title: IL-4/IL-13+TNF L48341_M2_TNF_1_02_I02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: AB8812


title: IL-4/IL-13 L49480_M2_2_05_H13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49475_M2_2_05_H08

description:
IL-4/IL-13
IL-4/IL-13


title: AB8810


title: IL-4/IL-13 L49477_M2_2_05_H10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49478_M2_2_05_H11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49474_M2_2_05_H07

description:
IL-4/IL-13
IL-4/IL-13


title: AB8813


title: T24_ctrl_1


title: AB8807


title: IL-4/IL-13 L49472_M2_2_05_H05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49484_M2_2_05_H17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49473_M2_2_05_H06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49471_M2_2_05_H04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49476_M2_2_05_H09

description:
IL-4/IL-13
IL-4/IL-13


title: AB8811


title: AB8806


title: AB8809


title: IL-4/IL-13 L49469_M2_2_05_H02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49468_M2_2_05_H01

description:
IL-4/IL-13
IL-4/IL-13


title: AB8802


title: IL-4/IL-13 L49479_M2_2_05_H12

description:
IL-4/IL-13
IL-4/IL-13


title: AB8804


title: AB8808


title: IL-4/IL-13 L49470_M2_2_05_H03

description:
IL-4/IL-13
IL-4/IL-13


title: AB8805


title: AB8801


title: AB8803


title: IL-4/IL-13 L49467_M2_2_05_G24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49466_M2_2_05_G23

description:
IL-4/IL-13
IL-4/IL-13


title: AB8799


title: AB8798


title: IL-4/IL-13 L49462_M2_2_05_G19

description:
IL-4/IL-13
IL-4/IL-13


title: AB8800


title: AB8797


title: IL-4/IL-13 L49463_M2_2_05_G20

description:
IL-4/IL-13
IL-4/IL-13


title: AB8421


title: AB8420


title: IL-4/IL-13 L49457_M2_2_05_G14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49456_M2_2_05_G13

description:
IL-4/IL-13
IL-4/IL-13


title: AB8795


title: AB8796


title: IL-4/IL-13 L49461_M2_2_05_G18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49460_M2_2_05_G17

description:
IL-4/IL-13
IL-4/IL-13


title: AB8416


title: IL-4/IL-13 L49455_M2_2_05_G12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49453_M2_2_05_G10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49454_M2_2_05_G11

description:
IL-4/IL-13
IL-4/IL-13


title: AB8414


title: IL-4/IL-13 L49459_M2_2_05_G16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49465_M2_2_05_G22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49464_M2_2_05_G21

description:
IL-4/IL-13
IL-4/IL-13


title: AB8413


title: AB8417


title: AB8418


title: AB8415


title: IL-4/IL-13 L49450_M2_2_05_G07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49452_M2_2_05_G09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49451_M2_2_05_G08

description:
IL-4/IL-13
IL-4/IL-13


title: AB8410


title: AB8412


title: AB8419


title: IL-4/IL-13 L49458_M2_2_05_G15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49449_M2_2_05_G06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49448_M2_2_05_G05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49446_M2_2_05_G03

description:
IL-4/IL-13
IL-4/IL-13


title: AB8407


title: IL-4/IL-13 L49447_M2_2_05_G04

description:
IL-4/IL-13
IL-4/IL-13


title: AB8405


title: IL-4/IL-13 L49443_M2_2_05_F24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49441_M2_2_05_F22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49442_M2_2_05_F23

description:
IL-4/IL-13
IL-4/IL-13


title: AB8404


title: IL-4/IL-13 L49445_M2_2_05_G02

description:
IL-4/IL-13
IL-4/IL-13


title: AB8131


title: AB8409


title: IL-4/IL-13 L49444_M2_2_05_G01

description:
IL-4/IL-13
IL-4/IL-13


title: AB8406


title: AB8408


title: AB8129


title: AB8403


title: IL-4/IL-13 L49440_M2_2_05_F21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49439_M2_2_05_F20

description:
IL-4/IL-13
IL-4/IL-13


title: AB8411


title: IL-4/IL-13 L49438_M2_2_05_F19

description:
IL-4/IL-13
IL-4/IL-13


title: AB8128


title: IL-4/IL-13 L49433_M2_2_05_F14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49437_M2_2_05_F18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49434_M2_2_05_F15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49436_M2_2_05_F17

description:
IL-4/IL-13
IL-4/IL-13


title: AB8127


title: IL-4/IL-13 L49435_M2_2_05_F16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49432_M2_2_05_F13

description:
IL-4/IL-13
IL-4/IL-13


title: AB8124


title: AB8123


title: AB8126


title: AB8121


title: AB8122


title: IL-4/IL-13 L49431_M2_2_05_F12

description:
IL-4/IL-13
IL-4/IL-13


title: AB8130


title: IL-4/IL-13 L49429_M2_2_05_F10

description:
IL-4/IL-13
IL-4/IL-13


title: AB8119


title: AB8120


title: IL-4/IL-13 L49427_M2_2_05_F08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49428_M2_2_05_F09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49426_M2_2_05_F07

description:
IL-4/IL-13
IL-4/IL-13


title: AB7609


title: AB8118


title: AB7608


title: IL-4/IL-13 L49425_M2_2_05_F06

description:
IL-4/IL-13
IL-4/IL-13


title: AB7601


title: AB7592


title: IL-4/IL-13 L49423_M2_2_05_F04

description:
IL-4/IL-13
IL-4/IL-13


title: AB7591


title: IL-4/IL-13 L49424_M2_2_05_F05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49422_M2_2_05_F03

description:
IL-4/IL-13
IL-4/IL-13


title: AB7590


title: IL-4/IL-13 L49421_M2_2_05_F02

description:
IL-4/IL-13
IL-4/IL-13


title: AB7586


title: AB7587


title: IL-4/IL-13 L49420_M2_2_05_F01

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49430_M2_2_05_F11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49419_M2_2_05_E24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49418_M2_2_05_E23

description:
IL-4/IL-13
IL-4/IL-13


title: AB7585


title: IL-4/IL-13 L49416_M2_2_05_E21

description:
IL-4/IL-13
IL-4/IL-13


title: AB7584


title: AB7582


title: IL-4/IL-13 L49417_M2_2_05_E22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49415_M2_2_05_E20

description:
IL-4/IL-13
IL-4/IL-13


title: AB7583


title: IL-4/IL-13 L49414_M2_2_05_E19

description:
IL-4/IL-13
IL-4/IL-13


title: AB7581


title: AB7579


title: AB7603


title: IL-4/IL-13 L49411_M2_2_05_E16

description:
IL-4/IL-13
IL-4/IL-13


title: AB7578


title: IL-4/IL-13 L49412_M2_2_05_E17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49410_M2_2_05_E15

description:
IL-4/IL-13
IL-4/IL-13


title: Specimen-T4

city: Bengbu

first: Zhaoyi

last: Lu

state: Anhui

address: 287 Changhuai Road

department: Department of Otolaryngology

country: China

institute: The First Affiliated Hospital of Bengbu Medical College

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Genome_build: hg19

source_name: nasopharyngeal carcinoma tissue

extract_protocol:
Total RNAs were extracted according to the manufacturer’s instruction (Invitrogen, CA,USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 134-160 bp PCR amplified fragments (corresponding to 14-40 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

value: nasopharyngeal tumor tissue

tag: group

value: NPC

tag: tnm stage

tag: Sex

value: male

tag: age

tag: ethnicity

value: Asian

tag: molecule subtype

value: tiRNA and tRF


title: IL-4/IL-13 L49408_M2_2_05_E13

description:
IL-4/IL-13
IL-4/IL-13

source_name: Bone marrow


title: Specimen-T3

tag: tissue


title: IL-4/IL-13 L49409_M2_2_05_E14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49407_M2_2_05_E12

description:
IL-4/IL-13
IL-4/IL-13


title: Specimen-T2


title: IL-4/IL-13 L49406_M2_2_05_E11

description:
IL-4/IL-13
IL-4/IL-13


title: Specimen-T1


title: Specimen-N4

source_name: mucosal tissue

value: nasopharyngeal normal tissue

value: control


title: Specimen-N3


title: IL-4/IL-13 L49405_M2_2_05_E10

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L49404_M2_2_05_E09

description:
IL-4/IL-13
IL-4/IL-13


title: Specimen-N2


title: IL-4/IL-13 L49403_M2_2_05_E08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49400_M2_2_05_E05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49402_M2_2_05_E07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49413_M2_2_05_E18

description:
IL-4/IL-13
IL-4/IL-13


title: DU12_PE

city: Tel-Aviv

first: Daniel

middle: H

last: Wreschner

address: Ramat Aviv

institute: Tel Aviv University

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the human genome (hg38) using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count (version 0.6.1p1) with stranded="reverse" option.
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Genome_build: hg38
Supplementary_files_format_and_content: Processed file include raw counts and DESeq2 normalized counts.

source_name: U87 glioblastoma cells expressing human LY6S-iso1 protein

growth_protocol: U87 cells were grown with DMEM cell growth medium supplemented with 10% fetal calf serum.

extract_protocol:
RNA was extracted from cells using the Qiagen RNA extraction kit.
Libraries were prepared using the TruSeq Stranded mRNA. Sequencing was done on a NextSeq mid output 150 cycles kit, allocating 20M reads per sample (Illumina; paired end read sequencing).

treatment_protocol: U87 cells were stably transfected either with controlpQCXIP vector or with pQCXIP vector coding for LY6-iso1 protein. Stable transfectants were selected by adding puromycin to the cell growth medium.

tag: cell line


title: IL-4/IL-13 L49401_M2_2_05_E06

description:
IL-4/IL-13
IL-4/IL-13


title: AB7580


title: IL-4/IL-13 L49399_M2_2_05_E04

description:
IL-4/IL-13
IL-4/IL-13


title: DU10_PE


title: DU11_PE


title: DU9_PE

source_name: U87 glioblastoma cells


title: AB7577


title: DU8_PE


title: IL-4/IL-13 L49397_M2_2_05_E02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49396_M2_2_05_E01

description:
IL-4/IL-13
IL-4/IL-13


title: technical replicate for 67 [67_Ctl-Vhcl_3mois_B]

city: Nantes

first: Xavier

last: Prieur

address: 8 quai Moncousu

country: France

institute: INSERM

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Genome_build: Mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: technical replicate for 67

growth_protocol: 8 weeks-old mice were injected with Tamoxifen or vehicle and killed 15 days, 30 days or 90 days after the first injection.

extract_protocol:
Total RNA from tissues was purified using Trizol (Life technology, les Ulis, France) according to the manufacturer’s instructions. Total RNA from cell samples were purified with the NucleoSpin RNA II (Macherey Nagel, Hoerdt, France).
the libraries was prepared from 10 ng of total RNA. 15 RNA samples were extracted from hiPS. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach, which enriches for 3’ends of cDNA. 100ng of full-length cDNAs was used as input to the Nextera DNA Sample Prep kit (ref FC-121-1030, Illumina), which enriches for 3′ends of cDNA. Size library is controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350-800bp was run on an Illumina HiSeq 2500 using a HiSeq Rapid SBS Kit v2 (50 cycles; FC-402-4022) and a HiSeq Rapid PE Cluster Kit v2 (PE-402-4002) according to manufacturer’s protocol (Denaturing and Diluting Libraries for the HiSeq® and GAIIx, Part # 15050107 v03 protocol, Illumina).

treatment_protocol: No othe treament has been applied

tag: strain background

value: 20 weeks-old

tag: genotype/time point

value: Bscl2lox/lox-90 days

value: inguinal white adipose tissue


title: IL-4/IL-13 L49395_M2_2_05_D24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49394_M2_2_05_D23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49398_M2_2_05_E03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49393_M2_2_05_D22

description:
IL-4/IL-13
IL-4/IL-13


title: Specimen-N1


title: IL-4/IL-13 L49392_M2_2_05_D21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49391_M2_2_05_D20

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 30 days [93_CRE-Tamox_3mois]

source_name: iATSKO - 30 days

value: iATSKO - 30 days


title: iATSKO - 30 days [94_CRE-Tamox_3mois]


title: iATSKO - 30 days [92_CRE-Tamox_3mois]


title: iATSKO - 30 days [91_CRE-Tamox_3mois]


title: IL-4/IL-13 L49390_M2_2_05_D19

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 30 days [90_CRE-Tamox_3mois]


title: DU7_PE


title: IL-4/IL-13 L49389_M2_2_05_D18

description:
IL-4/IL-13
IL-4/IL-13


title: technical replicate of Sample 90 [90_CRE-Tamox_3mois_B]

source_name: technical replicate of Sample 90


title: IL-4/IL-13 L49388_M2_2_05_D17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49383_M2_2_05_D12

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 30 days [89_CRE-Tamox_3mois]


title: IL-4/IL-13 L49387_M2_2_05_D16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49386_M2_2_05_D15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49384_M2_2_05_D13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49385_M2_2_05_D14

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [85_Ctl-Tamox_3mois]

source_name: Bscl2lox/lox+ tamoxifen -30 days

value: Bscl2lox/lox+ tamoxifen -30 days


title: Bscl2lox/lox+ tamoxifen -30 days [87_Ctl-Tamox_3mois]


title: Bscl2lox/lox+ tamoxifen -30 days [84_Ctl-Tamox_3mois]


title: IL-4/IL-13 L49382_M2_2_05_D11

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [82_Ctl-Tamox_3mois]


title: IL-4/IL-13 L49381_M2_2_05_D10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49379_M2_2_05_D08

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [80_Ctl-Tamox_3mois]


title: Bscl2lox/lox+ tamoxifen -30 days [86_Ctl-Tamox_3mois]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [77_CRE-Vhcl_3mois]

source_name: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days

value: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days


title: IL-4/IL-13 L49377_M2_2_05_D06

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [79_Ctl-Tamox_3mois]


title: iATSKO - 30 days [88_CRE-Tamox_3mois]


title: Bscl2lox/lox+ tamoxifen -30 days [78_Ctl-Tamox_3mois]


title: Bscl2lox/lox+ tamoxifen -30 days [81_Ctl-Tamox_3mois]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [74_CRE-Vhcl_3mois]


title: IL-4/IL-13 L49374_M2_2_05_D03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49380_M2_2_05_D09

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [73_CRE-Vhcl_3mois]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [72_CRE-Vhcl_3mois]


title: IL-4/IL-13 L49373_M2_2_05_D02

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [83_Ctl-Tamox_3mois]


title: IL-4/IL-13 L49371_M2_2_05_C24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49370_M2_2_05_C23

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [71_CRE-Vhcl_3mois]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [76_CRE-Vhcl_3mois]


title: IL-4/IL-13 L49375_M2_2_05_D04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49369_M2_2_05_C22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49378_M2_2_05_D07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49368_M2_2_05_C21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49376_M2_2_05_D05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49367_M2_2_05_C20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49366_M2_2_05_C19

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-90 days [69_Ctl-Vhcl_3mois]

source_name: Bscl2lox/lox-90 days


title: IL-4/IL-13 L49365_M2_2_05_C18

description:
IL-4/IL-13
IL-4/IL-13


title: Liver sample from sASH group (SM35088R)

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Liver sample from sASH group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor environment (v3.1) in R.3.6.3

label: biotin

source_name: liver biopsy sample

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: disease state

value: silent alcoholic steatohepatitis (sASH)

value: liver


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [75_CRE-Vhcl_3mois]


title: Bscl2lox/lox-90 days [68_Ctl-Vhcl_3mois]


title: IL-4/IL-13 L49364_M2_2_05_C17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49372_M2_2_05_D01

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-90 days [66_Ctl-Vhcl_3mois]


title: Bscl2lox/lox-90 days [67_Ctl-Vhcl_3mois]


title: IL-4/IL-13 L49363_M2_2_05_C16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49362_M2_2_05_C15

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-90 days [65_Ctl-Vhcl_3mois]


title: IL-4/IL-13 L49359_M2_2_05_C12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49361_M2_2_05_C14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49357_M2_2_05_C10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49360_M2_2_05_C13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49358_M2_2_05_C11

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-90 days [70_Ctl-Vhcl_3mois]


title: IL-4/IL-13 L49356_M2_2_05_C09

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 30 days [64_CRE-Tamox_1mois]

value: 12 weeks-old


title: Liver sample from sASH group (SBM)

description: Liver sample from sASH group


title: IL-4/IL-13 L49355_M2_2_05_C08

description:
IL-4/IL-13
IL-4/IL-13


title: Liver sample from sASH group (SK2)

description: Liver sample from sASH group


title: IL-4/IL-13 L49354_M2_2_05_C07

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 30 days [63_CRE-Tamox_1mois]


title: Liver sample from sASH group (SA7)

description: Liver sample from sASH group


title: iATSKO - 30 days [62_CRE-Tamox_1mois]


title: IL-4/IL-13 L49352_M2_2_05_C05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49353_M2_2_05_C06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49351_M2_2_05_C04

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 30 days [61_CRE-Tamox_1mois]


title: Liver sample from sASH group (M572)

description: Liver sample from sASH group


title: Liver sample from sASH group (S45470E)

description: Liver sample from sASH group


title: Liver sample from sASH group (S10532K)

description: Liver sample from sASH group